diff --git a/crates/contrib/schematic_macros/src/config/mod.rs b/crates/contrib/schematic_macros/src/config/mod.rs
index 77c216633..bd3021e3a 100644
--- a/crates/contrib/schematic_macros/src/config/mod.rs
+++ b/crates/contrib/schematic_macros/src/config/mod.rs
@@ -135,6 +135,44 @@ struct SchematicImplArgs<'a> {
     instrument: &'a TokenStream,
 }
 
+/// The body of a `schema_name` that says which instantiation it describes.
+///
+/// A schema names each type it expands and refers back to that name wherever
+/// the type appears again, so a name has to identify one type.
+/// A generic named after its base alone does not: `MergeableMap<ToolConfig>`
+/// and `MergeableMap<ToolParameterConfig>` would both answer `MergeableMap`,
+/// and a consumer resolving a reference by name would walk a value against
+/// whichever of them it met first.
+///
+/// The arguments are appended instead, so the two are `MergeableMap_ToolConfig`
+/// and `MergeableMap_ToolParameterConfig`.
+/// An argument with no name of its own (a primitive) contributes nothing, which
+/// leaves the base name for a type generic only over those.
+#[cfg(feature = "schema")]
+fn generate_schema_name(base: &str, generics: &syn::Generics) -> TokenStream {
+    let type_params = generics.type_params().map(|param| &param.ident);
+    let mut appends = type_params.peekable();
+
+    if appends.peek().is_none() {
+        return quote! { Some(#base.into()) };
+    }
+
+    let appends = appends.map(|ident| {
+        quote! {
+            if let Some(argument) = <#ident as schematic::Schematic>::schema_name() {
+                name.push('_');
+                name.push_str(&argument);
+            }
+        }
+    });
+
+    quote! {
+        let mut name = String::from(#base);
+        #(#appends)*
+        Some(name)
+    }
+}
+
 #[cfg(feature = "schema")]
 fn emit_schematic_impls(args: &SchematicImplArgs<'_>) -> TokenStream {
     let &SchematicImplArgs {
@@ -153,6 +191,9 @@ fn emit_schematic_impls(args: &SchematicImplArgs<'_>) -> TokenStream {
     let partial_schema_name = partial_name.to_string();
     let partial_schema_impl = crate::common::Container::generate_partial_schema(name, cfg.generics);
 
+    let schema_name_impl = generate_schema_name(&schema_name, cfg.generics);
+    let partial_schema_name_impl = generate_schema_name(&partial_schema_name, cfg.generics);
+
     // `schema_union_with` unions the derived schema with caller-supplied
     // variants, for a type that deserializes from more shapes than its fields
     // describe. Using it asserts the extra shapes are shorthands for the fields,
@@ -180,7 +221,7 @@ fn emit_schematic_impls(args: &SchematicImplArgs<'_>) -> TokenStream {
         #[automatically_derived]
         impl #impl_generics schematic::Schematic for #name #ty_generics #schematic_where {
             fn schema_name() -> Option<String> {
-                Some(#schema_name.into())
+                #schema_name_impl
             }
 
             #instrument
@@ -194,7 +235,7 @@ fn emit_schematic_impls(args: &SchematicImplArgs<'_>) -> TokenStream {
         #[automatically_derived]
         impl #impl_generics schematic::Schematic for #partial_name #ty_generics #partial_schematic_where {
             fn schema_name() -> Option<String> {
-                Some(#partial_schema_name.into())
+                #partial_schema_name_impl
             }
 
             #instrument
diff --git a/crates/jp_cli/src/cmd/conversation/print_tests.rs b/crates/jp_cli/src/cmd/conversation/print_tests.rs
index 9c91d8fe0..88a51f00a 100644
--- a/crates/jp_cli/src/cmd/conversation/print_tests.rs
+++ b/crates/jp_cli/src/cmd/conversation/print_tests.rs
@@ -70,14 +70,14 @@ fn tool_with_style(style: DisplayStyleConfig) -> ToolConfig {
         summary: None,
         description: None,
         examples: None,
-        parameters: IndexMap::new(),
+        parameters: IndexMap::new().into(),
         run: None,
         format: None,
         result: None,
         cancellation_response: None,
         style: Some(style),
-        questions: IndexMap::new(),
-        options: IndexMap::new(),
+        questions: IndexMap::new().into(),
+        options: IndexMap::new().into(),
         access: None,
     }
 }
diff --git a/crates/jp_cli/src/cmd/plugin/dispatch.rs b/crates/jp_cli/src/cmd/plugin/dispatch.rs
index 7ff21bb79..3066a7a93 100644
--- a/crates/jp_cli/src/cmd/plugin/dispatch.rs
+++ b/crates/jp_cli/src/cmd/plugin/dispatch.rs
@@ -937,7 +937,7 @@ async fn prepare_turn(
     // added to the workspace since then is otherwise unknown to it, and starting
     // it fails.
     ctx.mcp_client
-        .set_servers(config.providers.mcp.clone())
+        .set_servers(config.providers.mcp.clone().into_map())
         .await;
 
     // Shared, because a turn spawned earlier may still be using a server this
diff --git a/crates/jp_cli/src/cmd/query.rs b/crates/jp_cli/src/cmd/query.rs
index 1c59dca42..c48f13881 100644
--- a/crates/jp_cli/src/cmd/query.rs
+++ b/crates/jp_cli/src/cmd/query.rs
@@ -2558,12 +2558,12 @@ fn apply_enable_tools(
     for d in directives.iter() {
         match d {
             ToolDirective::EnableAll => {
-                for (name, tool) in &mut partial.conversation.tools.tools {
+                for (name, tool) in partial.conversation.tools.tools.iter_mut() {
                     apply_directive_to_tool(name, tool, &defaults, ToggleScope::Bulk, true)?;
                 }
             }
             ToolDirective::DisableAll => {
-                for (name, tool) in &mut partial.conversation.tools.tools {
+                for (name, tool) in partial.conversation.tools.tools.iter_mut() {
                     apply_directive_to_tool(name, tool, &defaults, ToggleScope::Bulk, false)?;
                 }
             }
diff --git a/crates/jp_cli/src/cmd/query/tool/builtins.rs b/crates/jp_cli/src/cmd/query/tool/builtins.rs
index 111f64e9a..d30a4a246 100644
--- a/crates/jp_cli/src/cmd/query/tool/builtins.rs
+++ b/crates/jp_cli/src/cmd/query/tool/builtins.rs
@@ -30,7 +30,8 @@ pub fn describe_tools() -> PartialToolConfig {
                 ..Default::default()
             })),
             ..Default::default()
-        })]),
+        })])
+        .into(),
         run: Some(RunMode::Unattended),
         style: Some(PartialDisplayStyleConfig {
             hidden: Some(true),
diff --git a/crates/jp_cli/src/cmd/query/tool/coordinator_tests.rs b/crates/jp_cli/src/cmd/query/tool/coordinator_tests.rs
index 6791930a6..0cb1b65ce 100644
--- a/crates/jp_cli/src/cmd/query/tool/coordinator_tests.rs
+++ b/crates/jp_cli/src/cmd/query/tool/coordinator_tests.rs
@@ -190,7 +190,8 @@ fn test_question_target_with_configured_question() {
                     target: Some(QuestionTarget::Assistant(Box::default())),
                     answer: None,
                 }
-            },
+            }
+            .into(),
             ..Default::default()
         },
         vec![],
@@ -247,7 +248,8 @@ fn test_static_answer_with_configured_answer() {
                     target: Some(QuestionTarget::User),
                     answer: None,
                 }
-            },
+            }
+            .into(),
             ..Default::default()
         },
         vec![],
diff --git a/crates/jp_cli/src/cmd/query/turn_loop_tests.rs b/crates/jp_cli/src/cmd/query/turn_loop_tests.rs
index 21ddaba91..a41646ca1 100644
--- a/crates/jp_cli/src/cmd/query/turn_loop_tests.rs
+++ b/crates/jp_cli/src/cmd/query/turn_loop_tests.rs
@@ -1390,11 +1390,11 @@ async fn test_tool_interrupt_menu_cancel_escalates() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -1539,11 +1539,11 @@ async fn test_tool_stop_on_interrupt_commits_responses_without_follow_up() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: Some(CUSTOM_CANCELLATION_RESPONSE.to_string()),
             });
@@ -1679,14 +1679,15 @@ async fn test_interrupt_during_tool_prompt_completes_turn_early() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
                 questions: IndexMap::from_iter([("confirm".to_string(), QuestionConfig {
                     target: QuestionTarget::User,
                     answer: None,
-                })]),
-                options: IndexMap::default(),
+                })])
+                .into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2021,11 +2022,11 @@ async fn test_tool_restart_on_interrupt() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2177,11 +2178,11 @@ async fn test_merged_stream_exits_after_tool_response() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2290,11 +2291,11 @@ async fn test_tool_call_with_run_mode_ask_approves() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2434,11 +2435,11 @@ async fn test_tool_call_with_run_mode_ask_skips() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2589,11 +2590,11 @@ async fn test_permission_prompt_follows_interactive_not_is_tty() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2716,11 +2717,11 @@ async fn test_tool_call_with_run_mode_unattended() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -2855,11 +2856,11 @@ async fn test_tool_call_with_run_mode_skip() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -3010,11 +3011,11 @@ async fn test_multiple_tools_with_different_run_modes() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -3031,11 +3032,11 @@ async fn test_multiple_tools_with_different_run_modes() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -3219,11 +3220,11 @@ async fn test_tool_call_returns_error() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -4526,11 +4527,11 @@ async fn test_parallel_tool_calls_rendered_atomically() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: fn_call_style.clone(),
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -4546,11 +4547,11 @@ async fn test_parallel_tool_calls_rendered_atomically() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: fn_call_style,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -4719,11 +4720,11 @@ async fn test_single_tool_call_rendered_with_args() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -4938,11 +4939,11 @@ fn talking_tool_config(names: &[&str]) -> AppConfig {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -5434,7 +5435,7 @@ async fn a_tool_can_opt_out_of_the_progress_window() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: Some(DisplayStyleConfig {
                     hidden: false,
@@ -5448,8 +5449,8 @@ async fn a_tool_can_opt_out_of_the_progress_window() {
                         results_file_link: None,
                     },
                 }),
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -5990,7 +5991,7 @@ fn inquiry_tool_config(questions: &[&str]) -> ToolConfig {
         summary: None,
         description: None,
         examples: None,
-        parameters: IndexMap::new(),
+        parameters: IndexMap::new().into(),
         result: None,
         style: None,
         questions: questions
@@ -6001,8 +6002,9 @@ fn inquiry_tool_config(questions: &[&str]) -> ToolConfig {
                     answer: None,
                 })
             })
-            .collect(),
-        options: IndexMap::default(),
+            .collect::<IndexMap<_, _>>()
+            .into(),
+        options: IndexMap::default().into(),
         access: None,
         cancellation_response: None,
     }
@@ -7108,11 +7110,11 @@ async fn test_parallel_tools_one_with_inquiry() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -7543,11 +7545,11 @@ async fn test_unavailable_tool_before_approved_does_not_panic() {
                 summary: None,
                 description: None,
                 examples: None,
-                parameters: IndexMap::new(),
+                parameters: IndexMap::new().into(),
                 result: None,
                 style: None,
-                questions: IndexMap::new(),
-                options: IndexMap::default(),
+                questions: IndexMap::new().into(),
+                options: IndexMap::default().into(),
                 access: None,
                 cancellation_response: None,
             });
@@ -7975,11 +7977,11 @@ async fn reasoning_before_a_tool_call_shades_the_tool_chrome() {
             summary: None,
             description: None,
             examples: None,
-            parameters: IndexMap::new(),
+            parameters: IndexMap::new().into(),
             result: None,
             style: None,
-            questions: IndexMap::new(),
-            options: IndexMap::default(),
+            questions: IndexMap::new().into(),
+            options: IndexMap::default().into(),
             access: None,
             cancellation_response: None,
         });
@@ -8101,11 +8103,11 @@ async fn a_tool_that_does_not_join_reasoning_renders_unshaded_live() {
             summary: None,
             description: None,
             examples: None,
-            parameters: IndexMap::new(),
+            parameters: IndexMap::new().into(),
             result: None,
             style: Some(non_joining_style()),
-            questions: IndexMap::new(),
-            options: IndexMap::default(),
+            questions: IndexMap::new().into(),
+            options: IndexMap::default().into(),
             access: None,
             cancellation_response: None,
         });
diff --git a/crates/jp_cli/src/cmd/query_tests.rs b/crates/jp_cli/src/cmd/query_tests.rs
index 5b99e741f..da9d092c0 100644
--- a/crates/jp_cli/src/cmd/query_tests.rs
+++ b/crates/jp_cli/src/cmd/query_tests.rs
@@ -48,7 +48,7 @@ use crate::{
 
 fn make_partial_with_tools() -> PartialAppConfig {
     let mut partial = PartialAppConfig::default();
-    partial.conversation.tools.tools = IndexMap::from_iter([
+    *partial.conversation.tools.tools = IndexMap::from_iter([
         ("implicitly_enabled_tool".into(), PartialToolConfig {
             enable: None,
             ..Default::default()
@@ -1204,7 +1204,7 @@ fn test_builtin_config_preserves_tool_order() {
     // Tool order is the order tools are presented to the provider, so merging
     // a builtin block must not move an existing entry to the end.
     let mut partial = PartialAppConfig::default();
-    partial.conversation.tools.tools = IndexMap::from_iter([
+    *partial.conversation.tools.tools = IndexMap::from_iter([
         ("describe_tools".into(), PartialToolConfig {
             result: Some(ResultMode::Ask),
             ..Default::default()
diff --git a/crates/jp_cli/src/config_pipeline_tests.rs b/crates/jp_cli/src/config_pipeline_tests.rs
index 2adf590e0..81351202e 100644
--- a/crates/jp_cli/src/config_pipeline_tests.rs
+++ b/crates/jp_cli/src/config_pipeline_tests.rs
@@ -264,6 +264,55 @@ fn conversation_clears_prevent_base_values_from_returning() {
     assert!(!partial.providers.mcp.contains_key("kagi"));
 }
 
+/// A server the conversation removed stays removed on the next invocation, with
+/// the paths taken from the delta rather than named by hand.
+///
+/// The two halves have to meet: the delta reports the key it dropped, and the
+/// pipeline clears it after filling.
+/// Either alone puts the server back, since filling reads a key the
+/// conversation does not hold as one it never mentioned.
+#[test]
+fn a_removed_server_survives_the_next_invocation() {
+    use jp_config::PartialConfigDelta as _;
+
+    let mut pipeline = empty_pipeline();
+    pipeline
+        .base
+        .providers
+        .mcp
+        .insert("bookworm".to_owned(), mcp_server("serve"));
+    pipeline
+        .base
+        .providers
+        .mcp
+        .insert("kagi".to_owned(), mcp_server("search"));
+
+    // The invocation that removed `kagi`, as the producer sees it: the
+    // conversation's state before, against the config the turn ran with.
+    let before = pipeline.base.clone();
+    let mut after = pipeline.base.clone();
+    after.providers.mcp.shift_remove("kagi");
+
+    let mut unsets = Vec::new();
+    let delta = before.delta_with_unsets(after.clone(), "", &mut unsets);
+
+    assert!(
+        !delta.providers.mcp.contains_key("kagi"),
+        "the delta carries the map the user is left with"
+    );
+
+    let partial = pipeline.partial_with_conversation(after, &unsets).unwrap();
+
+    assert!(
+        !partial.providers.mcp.contains_key("kagi"),
+        "the workspace must not restore a server the conversation removed"
+    );
+    assert!(
+        partial.providers.mcp.contains_key("bookworm"),
+        "and the servers it kept are still there"
+    );
+}
+
 #[test]
 fn conversation_clears_allow_explicit_cfg_values() {
     let mut pipeline = empty_pipeline();
diff --git a/crates/jp_cli/src/ctx.rs b/crates/jp_cli/src/ctx.rs
index 7ecbf6ab9..ddd57ca44 100644
--- a/crates/jp_cli/src/ctx.rs
+++ b/crates/jp_cli/src/ctx.rs
@@ -130,7 +130,7 @@ impl Ctx {
         let config = config.into();
         let escalation_cooldown =
             Duration::from_secs(config.interrupt.escalation_cooldown_secs.into());
-        let mcp_client = jp_mcp::Client::new(config.providers.mcp.clone())
+        let mcp_client = jp_mcp::Client::new(config.providers.mcp.clone().into_map())
             .with_child_cwd(exec.child_cwd().map(|cwd| cwd.as_std_path().to_path_buf()));
 
         let is_tty = io::stdout().is_terminal();
diff --git a/crates/jp_config/src/assignment.rs b/crates/jp_config/src/assignment.rs
index 632fc541b..8fe5c231f 100644
--- a/crates/jp_config/src/assignment.rs
+++ b/crates/jp_config/src/assignment.rs
@@ -12,7 +12,10 @@ use schematic::{MergeResult, PartialConfig};
 use serde::{Serialize, de::DeserializeOwned};
 use serde_json::{Value, from_str};
 
-use crate::{AppConfig, BoxedError, types::vec::MergeableVec};
+use crate::{
+    AppConfig, BoxedError,
+    types::{map::MergeableMap, vec::MergeableVec},
+};
 
 /// The result of assigning a key-value pair to a configuration.
 pub type AssignResult = Result<(), BoxedError>;
@@ -352,6 +355,39 @@ impl KvAssignment {
         Ok(())
     }
 
+    /// Assign a key-value pair to an entry of a map that carries its own merge
+    /// strategy.
+    ///
+    /// Mirrors [`Self::assign_to_entry`], with one more shape to tell apart: a
+    /// whole-map object carrying `value` beside `strategy` is the wrapper that
+    /// states how the map merges, not two entries named after those keys.
+    ///
+    /// Told apart by the test the map's own deserializer uses, so a strategy
+    /// written on the command line and one written in a config file mean the
+    /// same thing.
+    /// An entry named `value` needs the sibling `strategy` before it reads as
+    /// the wrapper, which keeps a tool called `value` assignable.
+    ///
+    /// Anything else is an entry, and lands inside whatever wrapper the map
+    /// already carries: naming one entry says nothing about how the map
+    /// combines.
+    pub(crate) fn assign_to_mergeable_entry<V>(self, map: &mut MergeableMap<V>) -> AssignResult
+    where
+        V: AssignKeyValue + Default + Clone + DeserializeOwned,
+    {
+        if self.key.is_empty()
+            && let KvValue::Json(Value::Object(object)) = &self.value
+            && object.contains_key("value")
+            && object.contains_key("strategy")
+        {
+            let value = self.value.clone().into_value();
+            *map = serde_json::from_value(value).map_err(|error| kv_error(&self.key, error))?;
+            return Ok(());
+        }
+
+        self.assign_to_entry(map)
+    }
+
     /// Parse an assignment from an environment variable.
     ///
     /// The environment variable is expected to be in the format
diff --git a/crates/jp_config/src/conversation.rs b/crates/jp_config/src/conversation.rs
index ebda01226..3cb18520c 100644
--- a/crates/jp_config/src/conversation.rs
+++ b/crates/jp_config/src/conversation.rs
@@ -14,16 +14,19 @@ use crate::{
     conversation::{
         attachment::{AttachmentConfig, PartialAttachmentConfig},
         compaction::{CompactionConfig, PartialCompactionConfig},
-        label::{LabelConfig, PartialLabelConfig},
+        label::LabelConfig,
         title::{PartialTitleConfig, TitleConfig},
         tool::{PartialToolsConfig, ToolsConfig},
     },
-    delta::{PartialConfigDelta, delta_mergeable_vec, delta_opt, delta_opt_at, path},
+    delta::{
+        PartialConfigDelta, delta_mergeable_map, delta_mergeable_map_at, delta_mergeable_vec,
+        delta_opt, delta_opt_at, path,
+    },
     fill::FillDefaults,
     internal::merge::{map_with_strategy, vec_with_strategy},
     partial::{ToPartial, partial_opt},
     types::{
-        map::{MergeableMap, MergedMap, MergedMapStrategy, map_to_mergeable_partial},
+        map::{MergeableMap, map_to_mergeable_partial},
         vec::{MergeableVec, MergedVec, vec_to_mergeable_partial},
     },
     validate::Validator,
@@ -121,7 +124,7 @@ impl AssignKeyValue for PartialConversationConfig {
             _ if kv.p("tools") => self.tools.assign(kv)?,
             _ if kv.p("compaction") => self.compaction.assign(kv)?,
             _ if kv.p("attachments") => kv.try_vec_of_nested(self.attachments.as_mut())?,
-            _ if kv.p("labels") => kv.assign_to_entry(&mut self.labels)?,
+            _ if kv.p("labels") => kv.assign_to_mergeable_entry(&mut self.labels)?,
             _ if kv.p("inquiry") => self.inquiry.assign(kv)?,
             _ if kv.p("start_local") => self.start_local = kv.try_some_bool()?,
             "default_id" => self.default_id = kv.try_some_from_str()?,
@@ -132,41 +135,6 @@ impl AssignKeyValue for PartialConversationConfig {
     }
 }
 
-impl PartialConversationConfig {
-    /// The label rules `next` changes.
-    fn labels_delta(
-        &self,
-        next: MergeableMap<PartialLabelConfig>,
-    ) -> MergeableMap<PartialLabelConfig> {
-        // A key in the previous state that is absent from the next one
-        // can only have been dropped by a replacing layer, and a
-        // minimal delta has no way to spell "removed": it carries
-        // entries, and a missing entry means "unchanged". Emit the
-        // whole wrapper in that case so the fold replaces the map
-        // instead of deep-merging the dropped rule back in.
-        let dropped = self.labels.keys().any(|key| !next.contains_key(key));
-
-        if dropped {
-            // Force replace semantics rather than trusting the shape
-            // `next` arrived in: a plain `Map` deep-merges on the fold
-            // and resurrects the dropped rule.
-            MergeableMap::Merged(MergedMap {
-                value: next.into_map(),
-                strategy: Some(MergedMapStrategy::Replace),
-                discard_when_merged: false,
-            })
-        } else {
-            next.into_iter()
-                .filter_map(|(key, next)| match self.labels.get(&key) {
-                    Some(prev) if prev == &next => None,
-                    Some(prev) => Some((key, prev.delta(next))),
-                    None => Some((key, next)),
-                })
-                .collect()
-        }
-    }
-}
-
 impl PartialConfigDelta for PartialConversationConfig {
     fn delta(&self, next: Self) -> Self {
         Self {
@@ -177,7 +145,7 @@ impl PartialConfigDelta for PartialConversationConfig {
             inquiry: self.inquiry.delta(next.inquiry),
             start_local: delta_opt(self.start_local.as_ref(), next.start_local),
             default_id: delta_opt(self.default_id.as_ref(), next.default_id),
-            labels: self.labels_delta(next.labels),
+            labels: delta_mergeable_map(&self.labels, next.labels),
         }
     }
 
@@ -186,7 +154,9 @@ impl PartialConfigDelta for PartialConversationConfig {
             title: self
                 .title
                 .delta_with_unsets(next.title, &path(prefix, "title"), unsets),
-            tools: self.tools.delta(next.tools),
+            tools: self
+                .tools
+                .delta_with_unsets(next.tools, &path(prefix, "tools"), unsets),
             compaction: self.compaction.delta(next.compaction),
             attachments: delta_mergeable_vec(&self.attachments, next.attachments),
             inquiry: self
@@ -199,7 +169,12 @@ impl PartialConfigDelta for PartialConversationConfig {
                 next.default_id,
                 unsets,
             ),
-            labels: self.labels_delta(next.labels),
+            labels: delta_mergeable_map_at(
+                &path(prefix, "labels"),
+                &self.labels,
+                next.labels,
+                unsets,
+            ),
         }
     }
 }
diff --git a/crates/jp_config/src/conversation/compaction.rs b/crates/jp_config/src/conversation/compaction.rs
index 42f7dfd05..f6a3c0d40 100644
--- a/crates/jp_config/src/conversation/compaction.rs
+++ b/crates/jp_config/src/conversation/compaction.rs
@@ -87,10 +87,17 @@ impl AssignKeyValue for PartialCompactionConfig {
 impl PartialConfigDelta for PartialCompactionConfig {
     fn delta(&self, next: Self) -> Self {
         Self {
-            // Not `delta_mergeable_vec`: the built-in defaults carry
-            // `discard_when_merged`, so an empty resolved list and the defaults
-            // compare unequal while resolving alike, and a replace-with-empty
-            // delta would be written for no change at all.
+            // Not `delta_mergeable_vec`, which would say `replace` for any
+            // difference: this field's partial is a bare `MergeableVec`, so an
+            // empty one is both "the user said nothing about rules" and "the
+            // user asked for no rules". A sparse partial (a `--model` override,
+            // say) carries the empty one, and replacing with it would record
+            // zero rules the user never asked for, making a later
+            // `jp conversation compact` a no-op.
+            //
+            // Telling the two apart needs the field's partial to be an
+            // `Option<MergeableVec<_>>`, as every converted list field has,
+            // where `None` is absent and `Some([])` is a deliberate empty.
             rules: {
                 next.rules
                     .into_iter()
diff --git a/crates/jp_config/src/conversation/tool.rs b/crates/jp_config/src/conversation/tool.rs
index d09eeb8c0..94d25a5ff 100644
--- a/crates/jp_config/src/conversation/tool.rs
+++ b/crates/jp_config/src/conversation/tool.rs
@@ -17,11 +17,18 @@ use crate::{
         access::{AccessConfig, PartialAccessConfig},
         style::{DisplayStyleConfig, PartialDisplayStyleConfig},
     },
-    delta::{PartialConfigDelta, delta_map, delta_opt, delta_opt_partial, delta_vec},
+    delta::{
+        PartialConfigDelta, delta_mergeable_map, delta_mergeable_map_at, delta_mergeable_value_map,
+        delta_mergeable_value_map_at, delta_opt, delta_opt_at, delta_opt_partial,
+        delta_opt_partial_at, delta_vec, path,
+    },
     fill::{FillDefaults, fill_map},
+    internal::merge::map_with_strategy,
     partial::{ToPartial, partial_opt, partial_opt_config, partial_opts},
-    types::json_value::JsonValue,
-    util::merge_nested_indexmap,
+    types::{
+        json_value::JsonValue,
+        map::{MergeableMap, map_to_partial_per_key},
+    },
     validate::Validator,
 };
 
@@ -43,8 +50,8 @@ pub struct ToolsConfig {
     /// This section configures individual tools.
     /// The key is the tool ID, and cannot contain a comma: a comma separates
     /// one tool ID from the next wherever several are named at once.
-    #[setting(nested, flatten, merge = merge_nested_indexmap)]
-    tools: IndexMap<String, ToolConfig>,
+    #[setting(nested, flatten, merge = map_with_strategy)]
+    tools: MergeableMap<ToolConfig>,
 }
 
 impl AssignKeyValue for PartialToolsConfig {
@@ -52,7 +59,7 @@ impl AssignKeyValue for PartialToolsConfig {
         match kv.key_string().as_str() {
             "" => kv.try_merge_object(self)?,
             _ if kv.p("*") => self.defaults.assign(kv)?,
-            _ => kv.assign_to_entry(&mut self.tools)?,
+            _ => kv.assign_to_mergeable_entry(&mut self.tools)?,
         }
 
         Ok(())
@@ -63,7 +70,16 @@ impl PartialConfigDelta for PartialToolsConfig {
     fn delta(&self, next: Self) -> Self {
         Self {
             defaults: self.defaults.delta(next.defaults),
-            tools: delta_map(&self.tools, next.tools),
+            tools: delta_mergeable_map(&self.tools, next.tools),
+        }
+    }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            defaults: self
+                .defaults
+                .delta_with_unsets(next.defaults, &path(prefix, "*"), unsets),
+            tools: delta_mergeable_map_at(prefix, &self.tools, next.tools, unsets),
         }
     }
 }
@@ -82,21 +98,41 @@ impl FillDefaults for PartialToolsConfig {
         // tool's grants must be complete where they are written, so the `*`
         // block applies whole or not at all, `fs` and `env` together (resolved
         // in `ToolConfigWithDefaults::access`).
-        let tools = self
-            .tools
-            .into_iter()
-            .map(|(name, mut tool)| {
-                tool.style = tool
-                    .style
-                    .map(|style| style.fill_from(tool_defaults.style.clone()));
+        let fill_style = |mut tool: PartialToolConfig| {
+            tool.style = tool
+                .style
+                .map(|style| style.fill_from(tool_defaults.style.clone()));
+            tool
+        };
 
-                (name, tool)
-            })
-            .collect();
+        let tools = match self.tools {
+            // A map that states a strategy said how it combines, so only its
+            // tools' styles are filled and no default tool joins them.
+            MergeableMap::Merged(mut merged) => {
+                merged.value = merged
+                    .value
+                    .into_iter()
+                    .map(|(name, tool)| (name, fill_style(tool)))
+                    .collect();
+
+                MergeableMap::Merged(merged)
+            }
+
+            // Key by key, so a tool only the defaults declare is added while
+            // one this layer already has keeps its own value.
+            MergeableMap::Map(entries) => {
+                let entries = entries
+                    .into_iter()
+                    .map(|(name, tool)| (name, fill_style(tool)))
+                    .collect();
+
+                fill_map(entries, defaults.tools.into_map()).into()
+            }
+        };
 
         Self {
             defaults: tool_defaults,
-            tools: fill_map(tools, defaults.tools),
+            tools,
         }
     }
 }
@@ -127,7 +163,8 @@ impl ToPartial for ToolsConfig {
 
                 (name.clone(), tool)
             })
-            .collect();
+            .collect::<IndexMap<_, _>>()
+            .into();
 
         Self::Partial { defaults, tools }
     }
@@ -219,7 +256,7 @@ fn reject_comma_in_tool_names(tools: &ToolsConfig) -> Result<(), ConfigError> {
 /// reporting; the `'*'` defaults make no claim about any individual tool, so
 /// they pass over builtin and MCP tools instead of failing the whole config.
 fn reject_access_on_non_local_tools(tools: &ToolsConfig) -> Result<(), ConfigError> {
-    for (name, tool) in &tools.tools {
+    for (name, tool) in tools.tools.iter() {
         if tool.access.is_none() {
             continue;
         }
@@ -363,6 +400,33 @@ impl PartialConfigDelta for PartialToolsDefaultsConfig {
             access: delta_opt_partial(self.access.as_ref(), next.access),
         }
     }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            enable: delta_opt_partial_at(
+                &path(prefix, "enable"),
+                self.enable.as_ref(),
+                next.enable,
+                unsets,
+            ),
+            run: delta_opt(self.run.as_ref(), next.run),
+            format: delta_opt(self.format.as_ref(), next.format),
+            result: delta_opt(self.result.as_ref(), next.result),
+            cancellation_response: delta_opt(
+                self.cancellation_response.as_ref(),
+                next.cancellation_response,
+            ),
+            style: self
+                .style
+                .delta_with_unsets(next.style, &path(prefix, "style"), unsets),
+            access: delta_opt_partial_at(
+                &path(prefix, "access"),
+                self.access.as_ref(),
+                next.access,
+                unsets,
+            ),
+        }
+    }
 }
 
 impl FillDefaults for PartialToolsDefaultsConfig {
@@ -470,8 +534,13 @@ pub struct ToolConfig {
     /// values, or forcing a specific value by setting a single enum value.
     /// You CANNOT change the type of the argument, its name, or any other
     /// properties that would break the tool's original argument expectations.
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub parameters: IndexMap<String, ToolParameterConfig>,
+    ///
+    /// Entries merge by key, so a parameter narrowed in a later layer joins the
+    /// ones an earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub parameters: MergeableMap<ToolParameterConfig>,
 
     /// How to run the tool.
     ///
@@ -517,16 +586,26 @@ pub struct ToolConfig {
     /// documented by the tool.
     /// For example, `fs_create_file` uses `overwrite_file` when a file already
     /// exists.
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub questions: IndexMap<String, QuestionConfig>,
+    ///
+    /// Entries merge by key, so a question configured in a later layer joins
+    /// the ones an earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub questions: MergeableMap<QuestionConfig>,
 
     /// Per-tool options passed to the tool at runtime.
     ///
     /// A free-form map of key-value pairs that configure tool behavior.
     /// Each tool defines its own supported options and defaults.
     /// Unknown options are silently forwarded.
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub options: IndexMap<String, JsonValue>,
+    ///
+    /// Entries merge by key, so an option set in a later layer joins the ones
+    /// an earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub options: MergeableMap<JsonValue>,
 
     /// Resource access grants for the tool.
     ///
@@ -558,7 +637,7 @@ impl AssignKeyValue for PartialToolConfig {
             "cancellation_response" => self.cancellation_response = kv.try_some_string()?,
             _ if kv.p("style") => self.style.assign(kv)?,
             "questions" => self.questions = kv.try_object()?,
-            _ if kv.p("options") => kv.assign_to_entry(&mut self.options)?,
+            _ if kv.p("options") => kv.assign_to_mergeable_entry(&mut self.options)?,
             _ if kv.p("access") => self.access.assign(kv)?,
             _ => return missing_key(&kv),
         }
@@ -576,7 +655,7 @@ impl PartialConfigDelta for PartialToolConfig {
             summary: delta_opt(self.summary.as_ref(), next.summary),
             description: delta_opt(self.description.as_ref(), next.description),
             examples: delta_opt(self.examples.as_ref(), next.examples),
-            parameters: delta_map(&self.parameters, next.parameters),
+            parameters: delta_mergeable_map(&self.parameters, next.parameters),
             run: delta_opt(self.run.as_ref(), next.run),
             format: delta_opt(self.format.as_ref(), next.format),
             result: delta_opt(self.result.as_ref(), next.result),
@@ -585,20 +664,69 @@ impl PartialConfigDelta for PartialToolConfig {
                 next.cancellation_response,
             ),
             style: delta_opt_partial(self.style.as_ref(), next.style),
-            questions: delta_map(&self.questions, next.questions),
-            options: next
-                .options
-                .into_iter()
-                .filter_map(|(name, next)| {
-                    if self.options.get(&name).is_some_and(|prev| prev == &next) {
-                        return None;
-                    }
-                    Some((name, next))
-                })
-                .collect(),
+            questions: delta_mergeable_map(&self.questions, next.questions),
+            options: delta_mergeable_value_map(&self.options, next.options),
             access: delta_opt_partial(self.access.as_ref(), next.access),
         }
     }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            source: delta_opt(self.source.as_ref(), next.source),
+            enable: delta_opt_partial_at(
+                &path(prefix, "enable"),
+                self.enable.as_ref(),
+                next.enable,
+                unsets,
+            ),
+            command: delta_opt_partial_at(
+                &path(prefix, "command"),
+                self.command.as_ref(),
+                next.command,
+                unsets,
+            ),
+            summary: delta_opt(self.summary.as_ref(), next.summary),
+            description: delta_opt(self.description.as_ref(), next.description),
+            examples: delta_opt(self.examples.as_ref(), next.examples),
+            parameters: delta_mergeable_map_at(
+                &path(prefix, "parameters"),
+                &self.parameters,
+                next.parameters,
+                unsets,
+            ),
+            run: delta_opt(self.run.as_ref(), next.run),
+            format: delta_opt(self.format.as_ref(), next.format),
+            result: delta_opt(self.result.as_ref(), next.result),
+            cancellation_response: delta_opt(
+                self.cancellation_response.as_ref(),
+                next.cancellation_response,
+            ),
+            style: delta_opt_partial_at(
+                &path(prefix, "style"),
+                self.style.as_ref(),
+                next.style,
+                unsets,
+            ),
+            questions: delta_mergeable_map_at(
+                &path(prefix, "questions"),
+                &self.questions,
+                next.questions,
+                unsets,
+            ),
+            options: delta_mergeable_value_map_at(
+                &path(prefix, "options"),
+                &self.options,
+                next.options,
+                unsets,
+            ),
+            access: delta_opt_partial_at(
+                &path(prefix, "access"),
+                self.access.as_ref(),
+                next.access,
+                unsets,
+            ),
+        }
+    }
 }
 
 impl ToPartial for ToolConfig {
@@ -612,11 +740,9 @@ impl ToPartial for ToolConfig {
             summary: partial_opts(self.summary.as_ref(), defaults.summary),
             description: partial_opts(self.description.as_ref(), defaults.description),
             examples: partial_opts(self.examples.as_ref(), defaults.examples),
-            parameters: self
-                .parameters
-                .iter()
-                .map(|(k, v)| (k.clone(), v.to_partial()))
-                .collect(),
+            // Per key rather than `replace`: an entry a later layer adds still
+            // reaches a conversation created before it existed.
+            parameters: map_to_partial_per_key(self.parameters.iter()),
             run: partial_opts(self.run.as_ref(), defaults.run),
             format: partial_opts(self.format.as_ref(), defaults.format),
             result: partial_opts(self.result.as_ref(), defaults.result),
@@ -625,16 +751,13 @@ impl ToPartial for ToolConfig {
                 defaults.cancellation_response,
             ),
             style: partial_opt_config(self.style.as_ref(), defaults.style),
-            questions: self
-                .questions
-                .iter()
-                .map(|(k, v)| (k.clone(), v.to_partial()))
-                .collect(),
-            options: self
-                .options
-                .iter()
-                .map(|(k, v)| (k.clone(), v.clone()))
-                .collect(),
+            questions: map_to_partial_per_key(self.questions.iter()),
+            options: MergeableMap::Map(
+                self.options
+                    .iter()
+                    .map(|(k, v)| (k.clone(), v.clone()))
+                    .collect(),
+            ),
             access: partial_opt_config(self.access.as_ref(), defaults.access),
         }
     }
@@ -718,10 +841,15 @@ pub struct ToolParameterConfig {
     /// MCP properties are merged by name.
     /// Entries here may narrow nested fields or add fields to local and
     /// built-in object parameters.
-    #[setting(nested, merge = merge_nested_indexmap)]
-    #[serde(default, skip_serializing_if = "IndexMap::is_empty")]
+    ///
+    /// Entries merge by key, so a property narrowed in a later layer joins the
+    /// ones an earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    #[serde(default, skip_serializing_if = "MergeableMap::is_empty")]
     #[expect(clippy::use_self, reason = "macro can't resolve `Self`")]
-    pub properties: IndexMap<String, ToolParameterConfig>,
+    pub properties: MergeableMap<ToolParameterConfig>,
 }
 
 impl PartialConfigDelta for PartialToolParameterConfig {
@@ -737,7 +865,66 @@ impl PartialConfigDelta for PartialToolParameterConfig {
             // any element has to record the whole list.
             enumeration: delta_opt(self.enumeration.as_ref(), next.enumeration),
             items: delta_opt(self.items.as_ref(), next.items),
-            properties: delta_map(&self.properties, next.properties),
+            properties: delta_mergeable_map(&self.properties, next.properties),
+        }
+    }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            kind: delta_opt_partial_at(
+                &path(prefix, "type"),
+                self.kind.as_ref(),
+                next.kind,
+                unsets,
+            ),
+            default: delta_opt_at(
+                &path(prefix, "default"),
+                self.default.as_ref(),
+                next.default,
+                unsets,
+            ),
+            required: delta_opt_at(
+                &path(prefix, "required"),
+                self.required.as_ref(),
+                next.required,
+                unsets,
+            ),
+            summary: delta_opt_at(
+                &path(prefix, "summary"),
+                self.summary.as_ref(),
+                next.summary,
+                unsets,
+            ),
+            description: delta_opt_at(
+                &path(prefix, "description"),
+                self.description.as_ref(),
+                next.description,
+                unsets,
+            ),
+            examples: delta_opt_at(
+                &path(prefix, "examples"),
+                self.examples.as_ref(),
+                next.examples,
+                unsets,
+            ),
+            enumeration: delta_opt_at(
+                &path(prefix, "enum"),
+                self.enumeration.as_ref(),
+                next.enumeration,
+                unsets,
+            ),
+            items: delta_opt_at(
+                &path(prefix, "items"),
+                self.items.as_ref(),
+                next.items,
+                unsets,
+            ),
+            properties: delta_mergeable_map_at(
+                &path(prefix, "properties"),
+                &self.properties,
+                next.properties,
+                unsets,
+            ),
         }
     }
 }
@@ -755,11 +942,7 @@ impl ToPartial for ToolParameterConfig {
             examples: partial_opts(self.examples.as_ref(), defaults.examples),
             enumeration: self.enumeration.clone(),
             items: self.items.as_ref().map(|v| Box::new(v.to_partial())),
-            properties: self
-                .properties
-                .iter()
-                .map(|(k, v)| (k.clone(), v.to_partial()))
-                .collect(),
+            properties: map_to_partial_per_key(self.properties.iter()),
         }
     }
 }
@@ -1133,7 +1316,7 @@ impl ToolConfigWithDefaults {
 
     /// Return the parameters of the tool.
     #[must_use]
-    pub const fn parameters(&self) -> &IndexMap<String, ToolParameterConfig> {
+    pub fn parameters(&self) -> &IndexMap<String, ToolParameterConfig> {
         &self.tool.parameters
     }
 
@@ -1216,13 +1399,13 @@ impl ToolConfigWithDefaults {
 
     /// Return the questions configuration of the tool.
     #[must_use]
-    pub const fn questions(&self) -> &IndexMap<String, QuestionConfig> {
+    pub fn questions(&self) -> &IndexMap<String, QuestionConfig> {
         &self.tool.questions
     }
 
     /// Return the per-tool options map.
     #[must_use]
-    pub const fn options(&self) -> &IndexMap<String, JsonValue> {
+    pub fn options(&self) -> &IndexMap<String, JsonValue> {
         &self.tool.options
     }
 
@@ -1664,6 +1847,23 @@ impl PartialConfigDelta for PartialEnableConfig {
             allow_toggle: delta_opt(self.allow_toggle.as_ref(), next.allow_toggle),
         }
     }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            state: delta_opt_at(
+                &path(prefix, "state"),
+                self.state.as_ref(),
+                next.state,
+                unsets,
+            ),
+            allow_toggle: delta_opt_at(
+                &path(prefix, "allow_toggle"),
+                self.allow_toggle.as_ref(),
+                next.allow_toggle,
+                unsets,
+            ),
+        }
+    }
 }
 
 impl ToPartial for EnableConfig {
diff --git a/crates/jp_config/src/conversation/tool/style.rs b/crates/jp_config/src/conversation/tool/style.rs
index 50182451b..1373da62a 100644
--- a/crates/jp_config/src/conversation/tool/style.rs
+++ b/crates/jp_config/src/conversation/tool/style.rs
@@ -30,7 +30,7 @@ use crate::{
     BoxedError,
     assignment::{AssignKeyValue, AssignResult, KvAssignment, missing_key},
     conversation::tool::CommandConfigOrString,
-    delta::{PartialConfigDelta, delta_opt},
+    delta::{PartialConfigDelta, delta_opt, delta_opt_at, path},
     fill::FillDefaults,
     partial::{ToPartial, partial_opt, partial_opts},
 };
@@ -179,6 +179,50 @@ impl PartialConfigDelta for PartialDisplayStyleConfig {
             error: self.error.delta(next.error),
         }
     }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            hidden: delta_opt_at(
+                &path(prefix, "hidden"),
+                self.hidden.as_ref(),
+                next.hidden,
+                unsets,
+            ),
+            joins_reasoning: delta_opt_at(
+                &path(prefix, "joins_reasoning"),
+                self.joins_reasoning.as_ref(),
+                next.joins_reasoning,
+                unsets,
+            ),
+            inline_results: delta_opt_at(
+                &path(prefix, "inline_results"),
+                self.inline_results.as_ref(),
+                next.inline_results,
+                unsets,
+            ),
+            results_file_link: delta_opt_at(
+                &path(prefix, "results_file_link"),
+                self.results_file_link.as_ref(),
+                next.results_file_link,
+                unsets,
+            ),
+            parameters: delta_opt_at(
+                &path(prefix, "parameters"),
+                self.parameters.as_ref(),
+                next.parameters,
+                unsets,
+            ),
+            print_stderr: delta_opt_at(
+                &path(prefix, "print_stderr"),
+                self.print_stderr.as_ref(),
+                next.print_stderr,
+                unsets,
+            ),
+            error: self
+                .error
+                .delta_with_unsets(next.error, &path(prefix, "error"), unsets),
+        }
+    }
 }
 
 impl FillDefaults for PartialDisplayStyleConfig {
@@ -246,6 +290,23 @@ impl PartialConfigDelta for PartialErrorStyleConfig {
             results_file_link: delta_opt(self.results_file_link.as_ref(), next.results_file_link),
         }
     }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            inline_results: delta_opt_at(
+                &path(prefix, "inline_results"),
+                self.inline_results.as_ref(),
+                next.inline_results,
+                unsets,
+            ),
+            results_file_link: delta_opt_at(
+                &path(prefix, "results_file_link"),
+                self.results_file_link.as_ref(),
+                next.results_file_link,
+                unsets,
+            ),
+        }
+    }
 }
 
 impl FillDefaults for PartialErrorStyleConfig {
diff --git a/crates/jp_config/src/conversation/tool_tests.rs b/crates/jp_config/src/conversation/tool_tests.rs
index dd4c2fd57..38dce8477 100644
--- a/crates/jp_config/src/conversation/tool_tests.rs
+++ b/crates/jp_config/src/conversation/tool_tests.rs
@@ -933,18 +933,21 @@ fn test_tools_config() {
 
     assert_eq!(
         p.tools,
-        IndexMap::<_, _>::from_iter(vec![("cargo_check".to_owned(), PartialToolConfig {
-            enable: Some(PartialEnableConfig::ON),
-            source: Some(ToolSource::Local { tool: None }),
-            ..Default::default()
-        })])
+        MergeableMap::from(IndexMap::<_, _>::from_iter(vec![(
+            "cargo_check".to_owned(),
+            PartialToolConfig {
+                enable: Some(PartialEnableConfig::ON),
+                source: Some(ToolSource::Local { tool: None }),
+                ..Default::default()
+            }
+        )]))
     );
 
     let kv = KvAssignment::try_from_cli("foo:", r#"{"source":"builtin"}"#).unwrap();
     p.assign(kv).unwrap();
     assert_eq!(
         p.tools,
-        IndexMap::<_, _>::from_iter(vec![
+        MergeableMap::from(IndexMap::<_, _>::from_iter(vec![
             ("cargo_check".to_owned(), PartialToolConfig {
                 enable: Some(PartialEnableConfig::ON),
                 source: Some(ToolSource::Local { tool: None }),
@@ -954,7 +957,97 @@ fn test_tools_config() {
                 source: Some(ToolSource::Builtin { tool: None }),
                 ..Default::default()
             })
-        ])
+        ]))
+    );
+}
+
+/// The tools map takes a strategy, even though its entries are flattened to sit
+/// directly under `conversation.tools`.
+#[test]
+fn tools_map_accepts_a_replace_strategy() {
+    let config: PartialToolsConfig = toml::from_str(
+        r#"
+        strategy = "replace"
+
+        [value.my_tool]
+        source = "builtin"
+        "#,
+    )
+    .expect("a strategy-carrying tools map parses");
+
+    assert!(
+        matches!(&config.tools, MergeableMap::Merged(merged)
+            if merged.strategy == Some(crate::types::map::MergedMapStrategy::Replace)),
+        "expected the declared strategy to survive the flatten: {:?}",
+        config.tools
+    );
+    assert!(config.tools.contains_key("my_tool"));
+}
+
+/// The strategy a config file states is the strategy `--cfg` states.
+///
+/// The two spellings reach different code — one the map's deserializer, the
+/// other the key-value dispatch — and the doc comments advertise the wrapper
+/// without saying which of them it is for.
+#[test]
+fn a_map_strategy_means_the_same_through_cfg_as_through_toml() {
+    use crate::types::map::MergedMapStrategy;
+
+    let from_toml: PartialToolsConfig = toml::from_str(
+        r#"
+        [cargo_check.options]
+        value = { profile = "release" }
+        strategy = "replace"
+        "#,
+    )
+    .expect("a strategy-carrying options map parses from TOML");
+
+    let mut from_cli = PartialToolsConfig::default();
+    let kv = KvAssignment::try_from_cli(
+        "cargo_check.options:",
+        r#"{"value":{"profile":"release"},"strategy":"replace"}"#,
+    )
+    .unwrap();
+    from_cli.assign(kv).unwrap();
+
+    for (source, config) in [("toml", &from_toml), ("cfg", &from_cli)] {
+        let options = &config.tools["cargo_check"].options;
+
+        assert!(
+            matches!(options, MergeableMap::Merged(merged)
+                if merged.strategy == Some(MergedMapStrategy::Replace)),
+            "{source}: the declared strategy is the map's, not an entry: {options:?}"
+        );
+        assert!(
+            options.contains_key("profile"),
+            "{source}: the option the user set is the one the tool receives: {options:?}"
+        );
+        assert!(
+            !options.contains_key("strategy"),
+            "{source}: the metadata is not an option: {options:?}"
+        );
+    }
+}
+
+/// A plain tools map keeps merging per key, and a tool may be named `value`.
+#[test]
+fn tools_map_without_a_strategy_merges_per_key() {
+    let config: PartialToolsConfig = toml::from_str(
+        r#"
+        [value]
+        source = "builtin"
+        "#,
+    )
+    .expect("a plain tools map parses");
+
+    assert!(
+        matches!(&config.tools, MergeableMap::Map(_)),
+        "expected a plain map: {:?}",
+        config.tools
+    );
+    assert!(
+        config.tools.contains_key("value"),
+        "`value` alone names a tool, since a strategy needs both keys"
     );
 }
 
diff --git a/crates/jp_config/src/delta.rs b/crates/jp_config/src/delta.rs
index a753246c6..d8d653a14 100644
--- a/crates/jp_config/src/delta.rs
+++ b/crates/jp_config/src/delta.rs
@@ -1,9 +1,11 @@
 //! Configuration delta calculation.
 
-use indexmap::IndexMap;
 use schematic::PartialConfig;
 
-use crate::types::vec::{MergeableVec, MergedVec, MergedVecStrategy};
+use crate::types::{
+    map::{MergeableMap, MergedMap, MergedMapStrategy},
+    vec::{MergeableVec, MergedVec, MergedVecStrategy},
+};
 
 /// Calculate the delta between two partial configurations.
 ///
@@ -110,6 +112,44 @@ fn repeats_an_element<T: PartialEq>(items: &[T]) -> bool {
         .any(|(index, item)| items[..index].contains(item))
 }
 
+/// Calculate the delta between two strategy-carrying maps.
+///
+/// An entry only `next` has is carried whole, an entry both maps have carries
+/// its own delta, and an entry whose delta is empty is left out: a missing
+/// entry already means "unchanged", so carrying an empty one reads as a change
+/// that isn't there.
+///
+/// A key `prev` has and `next` does not was dropped, which entries cannot
+/// spell.
+/// The whole map is then carried with `replace`, since a deep merge would
+/// resurrect the dropped key.
+///
+/// See [`delta_mergeable_map_at`] for the variant that also reports the paths
+/// it drops and clears, which a caller filling one layer from another needs.
+pub fn delta_mergeable_map<T>(prev: &MergeableMap<T>, next: MergeableMap<T>) -> MergeableMap<T>
+where
+    T: PartialConfigDelta + PartialEq,
+{
+    if prev.keys().any(|key| !next.contains_key(key)) {
+        return replace_with(next);
+    }
+
+    next.into_iter()
+        .filter_map(|(key, next)| {
+            let Some(prev) = prev.get(&key) else {
+                return Some((key, next));
+            };
+
+            if prev == &next {
+                return None;
+            }
+
+            let delta = prev.delta(next);
+            (!delta.is_empty()).then_some((key, delta))
+        })
+        .collect()
+}
+
 /// Calculate the delta between two optional strategy-carrying lists.
 ///
 /// Wraps [`delta_mergeable_vec`] for a field whose partial is
@@ -152,19 +192,31 @@ pub fn delta_opt_partial_at<T: PartialConfigDelta + PartialEq>(
     }
 }
 
-/// Calculate the delta between two maps, reporting each entry's unsets.
+/// Calculate the delta between two strategy-carrying maps, reporting what
+/// merging cannot reach.
 ///
-/// Mirrors [`delta_map`], descending into each entry with the entry's own
-/// dotted path so a field inside it reports where it lives.
-pub fn delta_map_with_unsets<V>(
+/// A dropped key is said twice, because two readers need it.
+/// The value says it by carrying `replace`, which is what the conversation's
+/// own fold applies.
+/// The path says it to a caller that fills this layer from another, where a key
+/// this layer does not hold is indistinguishable from one it never mentioned —
+/// and filling would put the dropped key back.
+///
+/// An entry both maps hold is diffed with its own dotted path, so a field
+/// cleared inside a surviving entry reports where it lives.
+pub fn delta_mergeable_map_at<T>(
     prefix: &str,
-    prev: &IndexMap<String, V>,
-    next: IndexMap<String, V>,
+    prev: &MergeableMap<T>,
+    next: MergeableMap<T>,
     unsets: &mut Vec<String>,
-) -> IndexMap<String, V>
+) -> MergeableMap<T>
 where
-    V: PartialConfigDelta + PartialEq,
+    T: PartialConfigDelta + PartialEq,
 {
+    if report_dropped_keys(prefix, prev, &next, unsets) {
+        return replace_with(next);
+    }
+
     next.into_iter()
         .filter_map(|(key, next)| {
             let Some(prev) = prev.get(&key) else {
@@ -185,6 +237,75 @@ where
         .collect()
 }
 
+/// Report every key `prev` holds and `next` does not, returning whether there
+/// were any.
+fn report_dropped_keys<T>(
+    prefix: &str,
+    prev: &MergeableMap<T>,
+    next: &MergeableMap<T>,
+    unsets: &mut Vec<String>,
+) -> bool {
+    let dropped: Vec<String> = prev
+        .keys()
+        .filter(|key| !next.contains_key(*key))
+        .map(|key| path(prefix, key))
+        .collect();
+
+    let any = !dropped.is_empty();
+    unsets.extend(dropped);
+    any
+}
+
+/// The whole map, stated as a replacement.
+///
+/// Stated rather than inherited from the map's shape: a plain map deep-merges
+/// on the fold and brings a dropped key back.
+fn replace_with<T>(next: MergeableMap<T>) -> MergeableMap<T> {
+    MergeableMap::Merged(MergedMap {
+        value: next.into_map(),
+        strategy: Some(MergedMapStrategy::Replace),
+        discard_when_merged: false,
+    })
+}
+
+/// Calculate the delta between two strategy-carrying maps of plain values,
+/// reporting the keys it drops.
+///
+/// Mirrors [`delta_mergeable_map_at`] for a map whose values carry no partial
+/// of their own, so an entry is compared and carried whole rather than diffed,
+/// and only a dropped key has a path to report.
+pub fn delta_mergeable_value_map_at<T: Clone + PartialEq>(
+    prefix: &str,
+    prev: &MergeableMap<T>,
+    next: MergeableMap<T>,
+    unsets: &mut Vec<String>,
+) -> MergeableMap<T> {
+    if report_dropped_keys(prefix, prev, &next, unsets) {
+        return replace_with(next);
+    }
+
+    next.into_iter()
+        .filter(|(key, next)| !prev.get(key).is_some_and(|prev| prev == next))
+        .collect()
+}
+
+/// Calculate the delta between two strategy-carrying maps of plain values.
+///
+/// Mirrors [`delta_mergeable_map`] for a map whose values carry no partial of
+/// their own, so an entry is compared and carried whole rather than diffed.
+pub fn delta_mergeable_value_map<T: Clone + PartialEq>(
+    prev: &MergeableMap<T>,
+    next: MergeableMap<T>,
+) -> MergeableMap<T> {
+    if prev.keys().any(|key| !next.contains_key(key)) {
+        return replace_with(next);
+    }
+
+    next.into_iter()
+        .filter(|(key, next)| !prev.get(key).is_some_and(|prev| prev == next))
+        .collect()
+}
+
 /// Calculate the delta between two optional values, reporting a cleared field.
 ///
 /// A value that went away cannot be expressed by merging: schematic keeps the
@@ -226,35 +347,6 @@ pub fn delta_opt_partial<T: PartialConfigDelta + PartialEq>(
     }
 }
 
-/// Calculate the delta between two maps of partial configurations.
-///
-/// An entry only `next` has is kept whole.
-/// An entry both maps have contributes its own delta, and is left out when that
-/// delta is empty.
-///
-/// Dropping the empty ones is what keeps [`PartialConfig::is_empty`] meaningful
-/// for the enclosing config: a map counts as empty only when it has no entries
-/// at all, so an entry that carries no values still reads as a change.
-pub fn delta_map<V>(prev: &IndexMap<String, V>, next: IndexMap<String, V>) -> IndexMap<String, V>
-where
-    V: PartialConfigDelta + PartialEq,
-{
-    next.into_iter()
-        .filter_map(|(key, next)| {
-            let Some(prev) = prev.get(&key) else {
-                return Some((key, next));
-            };
-
-            if prev == &next {
-                return None;
-            }
-
-            let delta = prev.delta(next);
-            (!delta.is_empty()).then_some((key, delta))
-        })
-        .collect()
-}
-
 /// Calculate the delta between two vectors that merge by appending.
 ///
 /// The delta holds the elements `next` adds to `prev`.
diff --git a/crates/jp_config/src/delta_law_tests.rs b/crates/jp_config/src/delta_law_tests.rs
index 0d99ffe09..ddcd58622 100644
--- a/crates/jp_config/src/delta_law_tests.rs
+++ b/crates/jp_config/src/delta_law_tests.rs
@@ -81,35 +81,27 @@ fn assert_law(before: &[&str], after: &[&str]) {
 
 /// Fields whose clear is known not to survive a fold, and why.
 ///
-/// `conversation.compaction.rules` has built-in defaults carrying
-/// `discard_when_merged`, so a resolved empty list and the resolved defaults
-/// compare unequal while resolving alike.
-/// A delta helper that judged them by their elements would write a
-/// replace-with-empty for no change at all, which is how it was found: routing
-/// it through [`delta_mergeable_vec`] turned 39 tests red with exactly that
-/// noise.
+/// `conversation.compaction.rules` keeps its rules in a bare `MergeableVec`, so
+/// an empty one cannot say whether the user asked for no rules or said nothing
+/// about them.
+/// A delta that replaced on any difference would record zero rules from any
+/// sparse partial that reached it, which is how it was found: routing it
+/// through [`delta_mergeable_vec`] wrote `replace` with an empty list into 37
+/// snapshots and appended an event that should not exist.
+/// Reaching it needs the partial to be an `Option<MergeableVec<_>>`, as every
+/// converted list field has.
 ///
 /// `model.parameters.other` is the catch-all arm of its own key-value dispatch,
 /// so `parameters.other` names a key *inside* the map rather than the map
 /// itself, and clearing removes an entry that was never there.
 /// Reaching the whole field needs a path vocabulary that can say "this map"
 /// where the map is also the fallback.
-///
-/// `conversation.tools.*` addresses the tool defaults block, whose types have
-/// no path-reporting delta yet.
-/// Mechanical to add, and left for the pass that does the tool config as a
-/// whole.
 const CLEAR_NOT_RECORDED: &[&str] = &[
     "conversation.compaction.rules",
     "assistant.model.parameters.other",
     "style.reasoning.summary_model.parameters.other",
     "conversation.inquiry.assistant.model.parameters.other",
     "conversation.title.generate.model.parameters.other",
-    "conversation.tools.*.enable",
-    "conversation.tools.*.enable.state",
-    "conversation.tools.*.enable.allow_toggle",
-    "conversation.tools.*.style.error.inline_results",
-    "conversation.tools.*.style.error.results_file_link",
 ];
 
 /// Set `path` to whichever of a few generic values it accepts.
diff --git a/crates/jp_config/src/delta_tests.rs b/crates/jp_config/src/delta_tests.rs
index 2a653477e..9741b3045 100644
--- a/crates/jp_config/src/delta_tests.rs
+++ b/crates/jp_config/src/delta_tests.rs
@@ -4,7 +4,10 @@ use test_log::test;
 use super::*;
 use crate::{
     providers::mcp::{PartialMcpProviderConfig, PartialStdioConfig},
-    types::vec::{MergeableVec, MergedVec, MergedVecStrategy},
+    types::{
+        map::{MergeableMap, MergedMapStrategy},
+        vec::{MergeableVec, MergedVec, MergedVecStrategy},
+    },
 };
 
 /// A server entry with `arguments` set and every other field unset.
@@ -23,10 +26,78 @@ fn server(arguments: &[&str]) -> PartialMcpProviderConfig {
 }
 
 /// A one-server map, keyed as `kagi`.
-fn map(arguments: &[&str]) -> IndexMap<String, PartialMcpProviderConfig> {
+fn map(arguments: &[&str]) -> MergeableMap<PartialMcpProviderConfig> {
     let mut map = IndexMap::new();
     map.insert("kagi".to_owned(), server(arguments));
-    map
+    map.into()
+}
+
+/// A field cleared inside an entry both maps hold reports where it lives.
+///
+/// No key disappears, so the map merges per key and the entry carries its own
+/// delta.
+/// That delta cannot say a field went away, which is what the path is for.
+#[test]
+fn map_delta_reports_a_field_cleared_inside_a_surviving_entry() {
+    use crate::providers::mcp::{PartialChecksumConfig, PartialStdioConfig};
+
+    let with_checksum = |checksum: Option<PartialChecksumConfig>| {
+        let mut map = IndexMap::new();
+        map.insert(
+            "kagi".to_owned(),
+            PartialMcpProviderConfig::Stdio(PartialStdioConfig {
+                command: Some("serve".into()),
+                checksum,
+                ..PartialStdioConfig::default()
+            }),
+        );
+        MergeableMap::from(map)
+    };
+
+    let prev = with_checksum(Some(PartialChecksumConfig {
+        value: Some("abc".to_owned()),
+        ..PartialChecksumConfig::default()
+    }));
+
+    let mut unsets = Vec::new();
+    let delta = delta_mergeable_map_at("providers.mcp", &prev, with_checksum(None), &mut unsets);
+
+    assert_eq!(unsets, ["providers.mcp.kagi.checksum"]);
+    assert!(
+        !delta.is_empty(),
+        "the entry is carried so the clear has somewhere to land: {delta:?}"
+    );
+}
+
+/// A removed entry is carried as a `replace`, since a deep merge would bring
+/// the key back.
+#[test]
+fn map_delta_replaces_when_an_entry_is_removed() {
+    let prev = map(&["--a"]);
+    let next = MergeableMap::default();
+
+    let delta = delta_mergeable_map(&prev, next);
+
+    assert!(
+        matches!(&delta, MergeableMap::Merged(merged)
+            if merged.strategy == Some(MergedMapStrategy::Replace) && merged.value.is_empty()),
+        "expected an empty map stated as `replace`, got: {delta:?}"
+    );
+}
+
+/// An entry both maps hold is diffed, not replaced.
+#[test]
+fn map_delta_diffs_a_surviving_entry() {
+    let prev = map(&["--a"]);
+    let next = map(&["--a", "--b"]);
+
+    let delta = delta_mergeable_map(&prev, next);
+
+    assert!(
+        matches!(&delta, MergeableMap::Map(_)),
+        "no key went away, so the map merges per key: {delta:?}"
+    );
+    assert_eq!(delta.len(), 1);
 }
 
 /// The `arguments` of a server entry, for asserting on a computed delta.
@@ -254,10 +325,10 @@ fn a_dropped_stop_word_is_recorded_at_every_site() {
 
 #[test]
 fn map_delta_keeps_an_entry_only_next_has() {
-    let prev = IndexMap::new();
+    let prev = MergeableMap::default();
     let next = map(&["--a"]);
 
-    assert_eq!(delta_map(&prev, next.clone()), next);
+    assert_eq!(delta_mergeable_map(&prev, next.clone()), next);
 }
 
 #[test]
@@ -265,7 +336,7 @@ fn map_delta_keeps_the_changed_fields_of_an_entry() {
     let prev = map(&["--a"]);
     let next = map(&["--a", "--b"]);
 
-    let delta = delta_map(&prev, next);
+    let delta = delta_mergeable_map(&prev, next);
 
     assert_eq!(delta.len(), 1);
     assert_eq!(arguments(&delta["kagi"]), Some(&vec!["--b".to_owned()]));
@@ -279,7 +350,7 @@ fn map_delta_keeps_the_changed_fields_of_an_entry() {
 /// can now say `replace`, so the case is built directly.
 #[test]
 fn map_delta_drops_an_entry_whose_delta_is_empty() {
-    let entry = |command: &str| -> IndexMap<String, PartialMcpProviderConfig> {
+    let entry = |command: &str| -> MergeableMap<PartialMcpProviderConfig> {
         let mut map = IndexMap::new();
         map.insert(
             "kagi".to_owned(),
@@ -288,13 +359,13 @@ fn map_delta_drops_an_entry_whose_delta_is_empty() {
                 ..PartialStdioConfig::default()
             }),
         );
-        map
+        map.into()
     };
 
     // Equal entries are dropped by the equality check ahead of the delta.
-    assert!(delta_map(&entry("serve"), entry("serve")).is_empty());
+    assert!(delta_mergeable_map(&entry("serve"), entry("serve")).is_empty());
 
     // A differing entry contributes only what changed.
-    let delta = delta_map(&entry("serve"), entry("other"));
+    let delta = delta_mergeable_map(&entry("serve"), entry("other"));
     assert_eq!(delta.len(), 1);
 }
diff --git a/crates/jp_config/src/lib.rs b/crates/jp_config/src/lib.rs
index 1dcdb2453..2221eb4b1 100644
--- a/crates/jp_config/src/lib.rs
+++ b/crates/jp_config/src/lib.rs
@@ -316,13 +316,21 @@ impl PartialConfigDelta for PartialAppConfig {
                 &delta_path(prefix, "editor"),
                 unsets,
             ),
-            template: self.template.delta(next.template),
+            template: self.template.delta_with_unsets(
+                next.template,
+                &delta_path(prefix, "template"),
+                unsets,
+            ),
             providers: self.providers.delta_with_unsets(
                 next.providers,
                 &delta_path(prefix, "providers"),
                 unsets,
             ),
-            plugins: self.plugins.delta(next.plugins),
+            plugins: self.plugins.delta_with_unsets(
+                next.plugins,
+                &delta_path(prefix, "plugins"),
+                unsets,
+            ),
             user: self
                 .user
                 .delta_with_unsets(next.user, &delta_path(prefix, "user"), unsets),
diff --git a/crates/jp_config/src/lib_tests.rs b/crates/jp_config/src/lib_tests.rs
index 376f40fa3..9e7038ee2 100644
--- a/crates/jp_config/src/lib_tests.rs
+++ b/crates/jp_config/src/lib_tests.rs
@@ -772,6 +772,119 @@ fn a_dropped_mcp_argument_is_recorded() {
     );
 }
 
+/// A server the user removed is recorded twice over, so the conversation stops
+/// starting it.
+///
+/// Entries merge by key, which is what lets a server the workspace config
+/// gained reach a conversation created before it existed.
+/// That same property means a deep merge would resurrect a removed one, so the
+/// delta states `replace` and carries the map the user is left with.
+///
+/// The value settles the conversation's own fold.
+/// The path settles the layer above it, where the conversation is filled from
+/// the config files and a server it does not hold would otherwise read as one
+/// it never mentioned.
+#[test]
+fn a_removed_mcp_server_is_recorded() {
+    use crate::providers::mcp::{McpProviderConfig, StdioConfig};
+
+    let mut prev = AppConfig::new_test();
+    prev.providers.mcp.insert(
+        "bookworm".to_owned(),
+        McpProviderConfig::Stdio(StdioConfig {
+            command: "just".into(),
+            arguments: vec!["serve".to_owned()],
+            variables: vec![],
+            checksum: None,
+            optional: false,
+            startup_timeout_secs: 60,
+        }),
+    );
+
+    let mut next = prev.clone();
+    next.providers.mcp.shift_remove("bookworm");
+
+    let mut unsets = Vec::new();
+    let delta = prev
+        .to_partial()
+        .delta_with_unsets(next.to_partial(), "", &mut unsets);
+
+    assert_eq!(
+        unsets,
+        ["providers.mcp.bookworm"],
+        "the removed key reports its path, so filling cannot restore it"
+    );
+    assert!(
+        delta.providers.mcp.discard_when_merged() || !delta.providers.mcp.is_empty(),
+        "the delta carries the map the user is left with"
+    );
+
+    let mut folded = prev.to_partial();
+    folded.merge(&(), delta).expect("folding cannot fail");
+
+    assert!(
+        !crate::util::build(folded)
+            .expect("valid config")
+            .providers
+            .mcp
+            .contains_key("bookworm"),
+        "the server is gone after the fold"
+    );
+}
+
+/// A server only the workspace config declares reaches an existing
+/// conversation.
+///
+/// The conversation layer is a resolved snapshot merged over the layer built
+/// from the config files.
+/// Stating `replace` on that snapshot would drop every server the files declare
+/// and the conversation does not, so it merges per key instead.
+#[test]
+fn a_server_added_to_the_workspace_reaches_an_existing_conversation() {
+    use schematic::PartialConfig as _;
+
+    use crate::providers::mcp::{McpProviderConfig, StdioConfig};
+
+    let server = |command: &str| {
+        McpProviderConfig::Stdio(StdioConfig {
+            command: command.into(),
+            arguments: vec![],
+            variables: vec![],
+            checksum: None,
+            optional: false,
+            startup_timeout_secs: 60,
+        })
+    };
+
+    // The conversation was created knowing only `bookworm`.
+    let mut conversation = AppConfig::new_test();
+    conversation
+        .providers
+        .mcp
+        .insert("bookworm".to_owned(), server("just"));
+
+    // The workspace config has since gained `kagi`.
+    let mut files = PartialAppConfig::new_test();
+    files
+        .providers
+        .mcp
+        .insert("kagi".to_owned(), server("kagi").to_partial());
+
+    files
+        .merge(&(), conversation.to_partial())
+        .expect("merging cannot fail");
+    let resolved = crate::util::build(files).expect("valid config");
+
+    assert!(
+        resolved.providers.mcp.contains_key("kagi"),
+        "a server only the files declare survives the conversation layer"
+    );
+    assert!(
+        resolved.providers.mcp.contains_key("bookworm"),
+        "the conversation's own server survives too"
+    );
+}
+
 /// A union that names an expanded form contributes both the shorthand path and
 /// the expanded keys; a union of distinct values contributes only its path.
 ///
diff --git a/crates/jp_config/src/plugins.rs b/crates/jp_config/src/plugins.rs
index 801c433d2..09690363f 100644
--- a/crates/jp_config/src/plugins.rs
+++ b/crates/jp_config/src/plugins.rs
@@ -6,17 +6,17 @@
 
 pub mod command;
 
-use indexmap::IndexMap;
 use schematic::Config;
 
 use crate::{
     FillDefaults,
     assignment::{AssignKeyValue, AssignResult, KvAssignment, missing_key},
-    delta::PartialConfigDelta,
+    delta::{PartialConfigDelta, delta_mergeable_map, delta_mergeable_map_at, delta_opt, path},
     fill::fill_map,
+    internal::merge::map_with_strategy,
     partial::ToPartial,
     plugins::command::CommandPluginConfig,
-    util::merge_nested_indexmap,
+    types::map::{MergeableMap, map_to_partial_per_key},
 };
 
 /// Plugin configuration.
@@ -33,8 +33,13 @@ pub struct PluginsConfig {
     pub shutdown_timeout_secs: u16,
 
     /// Command plugin configurations, keyed by plugin name (e.g. `serve`).
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub command: IndexMap<String, CommandPluginConfig>,
+    ///
+    /// Entries merge by key, so a plugin configured in a later layer joins the
+    /// ones an earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub command: MergeableMap<CommandPluginConfig>,
 }
 
 impl AssignKeyValue for PartialPluginsConfig {
@@ -56,26 +61,29 @@ impl AssignKeyValue for PartialPluginsConfig {
 
 impl PartialConfigDelta for PartialPluginsConfig {
     fn delta(&self, next: Self) -> Self {
-        use crate::delta::delta_opt;
+        Self {
+            auto_install: delta_opt(self.auto_install.as_ref(), next.auto_install),
+            shutdown_timeout_secs: delta_opt(
+                self.shutdown_timeout_secs.as_ref(),
+                next.shutdown_timeout_secs,
+            ),
+            command: delta_mergeable_map(&self.command, next.command),
+        }
+    }
 
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
         Self {
             auto_install: delta_opt(self.auto_install.as_ref(), next.auto_install),
             shutdown_timeout_secs: delta_opt(
                 self.shutdown_timeout_secs.as_ref(),
                 next.shutdown_timeout_secs,
             ),
-            command: next
-                .command
-                .into_iter()
-                .filter_map(|(name, next)| {
-                    let next = match self.command.get(&name) {
-                        Some(prev) if prev == &next => return None,
-                        Some(prev) => prev.delta(next),
-                        None => next,
-                    };
-                    Some((name, next))
-                })
-                .collect(),
+            command: delta_mergeable_map_at(
+                &path(prefix, "command"),
+                &self.command,
+                next.command,
+                unsets,
+            ),
         }
     }
 }
@@ -87,7 +95,13 @@ impl FillDefaults for PartialPluginsConfig {
             shutdown_timeout_secs: self
                 .shutdown_timeout_secs
                 .or(defaults.shutdown_timeout_secs),
-            command: fill_map(self.command, defaults.command),
+            // Key by key, so a plugin only the defaults declare is added
+            // while one this layer already has keeps its own value. A map
+            // that states a strategy is left alone.
+            command: match self.command {
+                merged @ MergeableMap::Merged(_) => merged,
+                MergeableMap::Map(entries) => fill_map(entries, defaults.command.into_map()).into(),
+            },
         }
     }
 }
@@ -102,11 +116,9 @@ impl ToPartial for PluginsConfig {
                 &self.shutdown_timeout_secs,
                 defaults.shutdown_timeout_secs,
             ),
-            command: self
-                .command
-                .iter()
-                .map(|(k, v)| (k.clone(), v.to_partial()))
-                .collect(),
+            // Per key rather than `replace`: a plugin the workspace config
+            // gained after this conversation was created still reaches it.
+            command: map_to_partial_per_key(self.command.iter()),
         }
     }
 }
diff --git a/crates/jp_config/src/providers.rs b/crates/jp_config/src/providers.rs
index cbb23b130..3d7af4df8 100644
--- a/crates/jp_config/src/providers.rs
+++ b/crates/jp_config/src/providers.rs
@@ -3,19 +3,19 @@
 pub mod llm;
 pub mod mcp;
 
-use indexmap::IndexMap;
 use schematic::{Config, ConfigError};
 
 use crate::{
     assignment::{AssignKeyValue, AssignResult, KvAssignment, missing_key},
-    delta::{PartialConfigDelta, delta_map, delta_map_with_unsets, path},
+    delta::{PartialConfigDelta, delta_mergeable_map, delta_mergeable_map_at, path},
     fill::{FillDefaults, fill_map},
+    internal::merge::map_with_strategy,
     partial::ToPartial,
     providers::{
         llm::{LlmProviderConfig, PartialLlmProviderConfig},
         mcp::McpProviderConfig,
     },
-    util::merge_nested_indexmap,
+    types::map::{MergeableMap, map_to_partial_per_key},
     validate::Validator,
 };
 
@@ -34,8 +34,20 @@ pub struct ProviderConfig {
     ///
     /// Configuration for Model Context Protocol (MCP) servers.
     /// The key is the server ID.
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub mcp: IndexMap<String, McpProviderConfig>,
+    ///
+    /// ```toml
+    /// [providers.mcp.bookworm]
+    /// type = "stdio"
+    /// command = "just"
+    /// arguments = ["serve-bookworm"]
+    /// ```
+    ///
+    /// Entries merge by key, so a server added to a later layer joins the ones
+    /// an earlier layer configured rather than replacing them.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub mcp: MergeableMap<McpProviderConfig>,
 }
 
 impl Validator for ProviderConfig {
@@ -49,7 +61,7 @@ impl AssignKeyValue for PartialProviderConfig {
         match kv.key_string().as_str() {
             "" => kv.try_merge_object(self)?,
             _ if kv.p("llm") => self.llm.assign(kv)?,
-            _ if kv.p("mcp") => kv.assign_to_entry(&mut self.mcp)?,
+            _ if kv.p("mcp") => kv.assign_to_mergeable_entry(&mut self.mcp)?,
             // _ if kv.p("tts") => self.tts.assign(kv)?,
             _ => return missing_key(&kv),
         }
@@ -65,7 +77,7 @@ impl PartialConfigDelta for PartialProviderConfig {
     fn delta(&self, next: Self) -> Self {
         Self {
             llm: self.llm.delta(next.llm),
-            mcp: delta_map(&self.mcp, next.mcp),
+            mcp: delta_mergeable_map(&self.mcp, next.mcp),
         }
     }
 
@@ -74,7 +86,7 @@ impl PartialConfigDelta for PartialProviderConfig {
             llm: self
                 .llm
                 .delta_with_unsets(next.llm, &path(prefix, "llm"), unsets),
-            mcp: delta_map_with_unsets(&path(prefix, "mcp"), &self.mcp, next.mcp, unsets),
+            mcp: delta_mergeable_map_at(&path(prefix, "mcp"), &self.mcp, next.mcp, unsets),
         }
     }
 }
@@ -83,7 +95,14 @@ impl FillDefaults for PartialProviderConfig {
     fn fill_from(self, defaults: Self) -> Self {
         Self {
             llm: self.llm.fill_from(defaults.llm),
-            mcp: fill_map(self.mcp, defaults.mcp),
+            // Key by key, so a server only the defaults declare is added
+            // while one this layer already has keeps its own value. A map
+            // that states a strategy is left alone: its owner said how it
+            // combines, and filling gaps into it would answer differently.
+            mcp: match self.mcp {
+                merged @ MergeableMap::Merged(_) => merged,
+                MergeableMap::Map(entries) => fill_map(entries, defaults.mcp.into_map()).into(),
+            },
         }
     }
 }
@@ -92,11 +111,9 @@ impl ToPartial for ProviderConfig {
     fn to_partial(&self) -> Self::Partial {
         Self::Partial {
             llm: self.llm.to_partial(),
-            mcp: self
-                .mcp
-                .iter()
-                .map(|(k, v)| (k.clone(), v.to_partial()))
-                .collect(),
+            // Per key rather than `replace`: a server the workspace config
+            // gained after this conversation was created still reaches it.
+            mcp: map_to_partial_per_key(self.mcp.iter()),
         }
     }
 }
diff --git a/crates/jp_config/src/providers/llm.rs b/crates/jp_config/src/providers/llm.rs
index 6a834f760..bf8e1bf40 100644
--- a/crates/jp_config/src/providers/llm.rs
+++ b/crates/jp_config/src/providers/llm.rs
@@ -14,8 +14,9 @@ use schematic::{Config, ConfigError};
 
 use crate::{
     assignment::{AssignKeyValue, AssignResult, KvAssignment, missing_key},
-    delta::{PartialConfigDelta, delta_map, path},
+    delta::{PartialConfigDelta, delta_mergeable_map, delta_mergeable_map_at, path},
     fill::{FillDefaults, fill_map},
+    internal::merge::map_with_strategy,
     model::id::{ModelIdConfig, ModelIdConfigError, ModelIdOrAliasConfig, resolve_alias_chain},
     partial::ToPartial,
     providers::llm::{
@@ -28,7 +29,7 @@ use crate::{
         openai::{OpenaiConfig, PartialOpenaiConfig},
         openrouter::{OpenrouterConfig, PartialOpenrouterConfig},
     },
-    util::merge_nested_indexmap,
+    types::map::{MergeableMap, map_to_partial_per_key},
     validate::Validator,
 };
 
@@ -49,8 +50,13 @@ pub struct LlmProviderConfig {
     /// haiku = { provider = "anthropic", name = "claude-haiku-4-5" }
     /// coder = "opus"
     /// ```
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub aliases: IndexMap<String, ModelIdOrAliasConfig>,
+    ///
+    /// Entries merge by key, so an alias defined in a later layer joins the
+    /// ones an earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub aliases: MergeableMap<ModelIdOrAliasConfig>,
 
     /// Anthropic API configuration.
     #[setting(nested)]
@@ -95,7 +101,7 @@ impl AssignKeyValue for PartialLlmProviderConfig {
     fn assign(&mut self, mut kv: KvAssignment) -> AssignResult {
         match kv.key_string().as_str() {
             "" => kv.try_merge_object(self)?,
-            _ if kv.p("aliases") => kv.assign_to_entry(&mut self.aliases)?,
+            _ if kv.p("aliases") => kv.assign_to_mergeable_entry(&mut self.aliases)?,
             _ if kv.p("anthropic") => self.anthropic.assign(kv)?,
             _ if kv.p("cerebras") => self.cerebras.assign(kv)?,
             _ if kv.p("deepseek") => self.deepseek.assign(kv)?,
@@ -117,7 +123,7 @@ impl PartialConfigDelta for PartialLlmProviderConfig {
     // that drops the paths would merge a list onto the one already there.
     fn delta(&self, next: Self) -> Self {
         Self {
-            aliases: delta_map(&self.aliases, next.aliases),
+            aliases: delta_mergeable_map(&self.aliases, next.aliases),
             anthropic: self.anthropic.delta(next.anthropic),
             cerebras: self.cerebras.delta(next.cerebras),
             deepseek: self.deepseek.delta(next.deepseek),
@@ -131,7 +137,12 @@ impl PartialConfigDelta for PartialLlmProviderConfig {
 
     fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
         Self {
-            aliases: delta_map(&self.aliases, next.aliases),
+            aliases: delta_mergeable_map_at(
+                &path(prefix, "aliases"),
+                &self.aliases,
+                next.aliases,
+                unsets,
+            ),
             anthropic: self.anthropic.delta_with_unsets(
                 next.anthropic,
                 &path(prefix, "anthropic"),
@@ -155,7 +166,13 @@ impl PartialConfigDelta for PartialLlmProviderConfig {
 impl FillDefaults for PartialLlmProviderConfig {
     fn fill_from(self, defaults: Self) -> Self {
         Self {
-            aliases: fill_map(self.aliases, defaults.aliases),
+            // Key by key, so an alias only the defaults declare is added
+            // while one this layer already has keeps its own value. A map
+            // that states a strategy is left alone.
+            aliases: match self.aliases {
+                merged @ MergeableMap::Merged(_) => merged,
+                MergeableMap::Map(entries) => fill_map(entries, defaults.aliases.into_map()).into(),
+            },
             anthropic: self.anthropic.fill_from(defaults.anthropic),
             cerebras: self.cerebras.fill_from(defaults.cerebras),
             deepseek: self.deepseek.fill_from(defaults.deepseek),
@@ -171,11 +188,9 @@ impl FillDefaults for PartialLlmProviderConfig {
 impl ToPartial for LlmProviderConfig {
     fn to_partial(&self) -> Self::Partial {
         Self::Partial {
-            aliases: self
-                .aliases
-                .iter()
-                .map(|(k, v)| (k.clone(), v.to_partial()))
-                .collect(),
+            // Per key rather than `replace`: an alias the workspace config
+            // gained after this conversation was created still reaches it.
+            aliases: map_to_partial_per_key(self.aliases.iter()),
             anthropic: self.anthropic.to_partial(),
             cerebras: self.cerebras.to_partial(),
             deepseek: self.deepseek.to_partial(),
diff --git a/crates/jp_config/src/providers/mcp.rs b/crates/jp_config/src/providers/mcp.rs
index 2a3290e7b..bda87572e 100644
--- a/crates/jp_config/src/providers/mcp.rs
+++ b/crates/jp_config/src/providers/mcp.rs
@@ -7,7 +7,10 @@ use serde::{Deserialize, Serialize};
 
 use crate::{
     assignment::{AssignKeyValue, AssignResult, KvAssignment, missing_key},
-    delta::{PartialConfigDelta, delta_opt, delta_opt_mergeable_vec, delta_opt_partial},
+    delta::{
+        PartialConfigDelta, delta_opt, delta_opt_mergeable_vec, delta_opt_partial,
+        delta_opt_partial_at, path,
+    },
     internal::merge::ordered_vec_with_strategy,
     partial::{ToPartial, partial_opt, partial_opt_config},
     types::vec::MergeableVec,
@@ -47,8 +50,28 @@ impl PartialConfigDelta for PartialMcpProviderConfig {
         }
     }
 
-    // No `delta_with_unsets`: `arguments` and `variables` state `replace`
-    // themselves now, so no field here needs a path reported.
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        match (self, next) {
+            (Self::Stdio(prev), Self::Stdio(next)) => Self::Stdio(PartialStdioConfig {
+                command: delta_opt(prev.command.as_ref(), next.command),
+                // `arguments` and `variables` state `replace` themselves, so a
+                // dropped element travels in the value.
+                arguments: delta_opt_mergeable_vec(prev.arguments.as_ref(), next.arguments),
+                variables: delta_opt_mergeable_vec(prev.variables.as_ref(), next.variables),
+                checksum: delta_opt_partial_at(
+                    &path(prefix, "checksum"),
+                    prev.checksum.as_ref(),
+                    next.checksum,
+                    unsets,
+                ),
+                optional: delta_opt(prev.optional.as_ref(), next.optional),
+                startup_timeout_secs: delta_opt(
+                    prev.startup_timeout_secs.as_ref(),
+                    next.startup_timeout_secs,
+                ),
+            }),
+        }
+    }
 }
 
 impl McpProviderConfig {
diff --git a/crates/jp_config/src/schema_probe.rs b/crates/jp_config/src/schema_probe.rs
index 9fc0b14ce..27363b562 100644
--- a/crates/jp_config/src/schema_probe.rs
+++ b/crates/jp_config/src/schema_probe.rs
@@ -209,14 +209,17 @@ fn collect_type(
                 }
             }
         }
+        // A collection's contents sit below the keys that identify its variant,
+        // so the document is unambiguous there and the conservative fill
+        // applies, exactly as it does below a struct's own keys.
         SchemaType::Object(object) => {
             path.push(Step::MapEntry);
-            collect(&object.value_type, path, out, enclosing, strings);
+            collect(&object.value_type, path, out, enclosing, StringFill::Skip);
             path.pop();
         }
         SchemaType::Array(array) => {
             path.push(Step::Item);
-            collect(&array.items_type, path, out, enclosing, strings);
+            collect(&array.items_type, path, out, enclosing, StringFill::Skip);
             path.pop();
         }
         SchemaType::Union(union) => {
@@ -419,12 +422,12 @@ fn collect_rejections(
         }
         SchemaType::Object(object) => {
             path.push(Step::MapEntry);
-            collect_rejections(&object.value_type, path, out, enclosing, strings);
+            collect_rejections(&object.value_type, path, out, enclosing, StringFill::Skip);
             path.pop();
         }
         SchemaType::Array(array) => {
             path.push(Step::Item);
-            collect_rejections(&array.items_type, path, out, enclosing, strings);
+            collect_rejections(&array.items_type, path, out, enclosing, StringFill::Skip);
             path.pop();
         }
         SchemaType::Union(union) => {
diff --git a/crates/jp_config/src/snapshots/jp_config__tests__app_config_schema_shape.snap b/crates/jp_config/src/snapshots/jp_config__tests__app_config_schema_shape.snap
index 8bd969950..5a6bd931f 100644
--- a/crates/jp_config/src/snapshots/jp_config__tests__app_config_schema_shape.snap
+++ b/crates/jp_config/src/snapshots/jp_config__tests__app_config_schema_shape.snap
@@ -3,7 +3,7 @@ source: crates/jp_config/src/lib_tests.rs
 expression: "crate::schema_shape::render(&AppConfig::schema())"
 ---
 assistant: AssistantConfig
-  instructions?: MergeableVec
+  instructions?: MergeableVec_InstructionsConfig
     |:
       []: InstructionsConfig
         description: string | null
@@ -17,7 +17,7 @@ assistant: AssistantConfig
         items: [string]
         position?: int
         title: string | null
-    |: MergedVec
+    |: MergedVec_InstructionsConfig
       dedup?: "inherit" | "true" | "false" | bool | null
       discard_when_merged?: bool
       strategy?: "append" | "prepend" | "replace" | null
@@ -79,14 +79,14 @@ assistant: AssistantConfig
       separator?: "none" | "space" | "line" | "paragraph"
       strategy?: "append" | "prepend" | "replace"
       value?: string
-  system_prompt_sections?: MergeableVec
+  system_prompt_sections?: MergeableVec_SectionConfig
     |:
       []: SectionConfig
         content: string
         position?: int
         tag: string | null
         title: string | null
-    |: MergedVec
+    |: MergedVec_SectionConfig
       dedup?: "inherit" | "true" | "false" | bool | null
       discard_when_merged?: bool
       strategy?: "append" | "prepend" | "replace" | null
@@ -105,7 +105,7 @@ config_load_paths: MergeableVec
     strategy?: "append" | "prepend" | "replace" | null
     value?: [string]
 conversation: ConversationConfig
-  attachments?: MergeableVec
+  attachments?: MergeableVec_AttachmentConfig
     |:
       []: AttachmentConfig
         |: string
@@ -114,7 +114,7 @@ conversation: ConversationConfig
             *: unknown
           path: string
           type: string
-    |: MergedVec
+    |: MergedVec_AttachmentConfig
       dedup?: "inherit" | "true" | "false" | bool | null
       discard_when_merged?: bool
       strategy?: "append" | "prepend" | "replace" | null
@@ -127,7 +127,7 @@ conversation: ConversationConfig
             path: string
             type: string
   compaction: CompactionConfig
-    rules?: MergeableVec
+    rules?: MergeableVec_CompactionRuleConfig
       |:
         []: CompactionRuleConfig
           keep_first?: int | string
@@ -163,7 +163,13 @@ conversation: ConversationConfig
                           exclude?: bool
                       |: null
                     service_tier: "off" | "flex" | "standard" | "priority" | null
-                    stop_words?: @MergeableVec
+                    stop_words?: MergeableVec
+                      |: [string]
+                      |: MergedVec
+                        dedup?: "inherit" | "true" | "false" | bool | null
+                        discard_when_merged?: bool
+                        strategy?: "append" | "prepend" | "replace" | null
+                        value?: [string]
                     temperature: float | null
                     top_k: int | null
                     top_p: float | null
@@ -177,7 +183,7 @@ conversation: ConversationConfig
                 over: int | string
                 policy: "strip" (aka s) | "strip-responses" (aka strip_responses, sres) | "strip-requests" (aka strip_requests, sreq) | "omit" (aka o)
             |: null
-      |: MergedVec
+      |: MergedVec_CompactionRuleConfig
         dedup?: "inherit" | "true" | "false" | bool | null
         discard_when_merged?: bool
         strategy?: "append" | "prepend" | "replace" | null
@@ -216,7 +222,13 @@ conversation: ConversationConfig
                             exclude?: bool
                         |: null
                       service_tier: "off" | "flex" | "standard" | "priority" | null
-                      stop_words?: @MergeableVec
+                      stop_words?: MergeableVec
+                        |: [string]
+                        |: MergedVec
+                          dedup?: "inherit" | "true" | "false" | bool | null
+                          discard_when_merged?: bool
+                          strategy?: "append" | "prepend" | "replace" | null
+                          value?: [string]
                       temperature: float | null
                       top_k: int | null
                       top_p: float | null
@@ -233,7 +245,7 @@ conversation: ConversationConfig
   default_id: "ask" | "last-activated" (aka last, last_activated) | "last-created" (aka last_created) | "previous" (aka prev) | string | null
   inquiry: InquiryConfig
     assistant: AssistantConfig
-      instructions?: MergeableVec
+      instructions?: MergeableVec_InstructionsConfig
         |:
           []: InstructionsConfig
             description: string | null
@@ -247,7 +259,7 @@ conversation: ConversationConfig
             items: [string]
             position?: int
             title: string | null
-        |: MergedVec
+        |: MergedVec_InstructionsConfig
           dedup?: "inherit" | "true" | "false" | bool | null
           discard_when_merged?: bool
           strategy?: "append" | "prepend" | "replace" | null
@@ -309,14 +321,14 @@ conversation: ConversationConfig
           separator?: "none" | "space" | "line" | "paragraph"
           strategy?: "append" | "prepend" | "replace"
           value?: string
-      system_prompt_sections?: MergeableVec
+      system_prompt_sections?: MergeableVec_SectionConfig
         |:
           []: SectionConfig
             content: string
             position?: int
             tag: string | null
             title: string | null
-        |: MergedVec
+        |: MergedVec_SectionConfig
           dedup?: "inherit" | "true" | "false" | bool | null
           discard_when_merged?: bool
           strategy?: "append" | "prepend" | "replace" | null
@@ -327,7 +339,7 @@ conversation: ConversationConfig
               tag: string | null
               title: string | null
       tool_choice?: "auto" | "none" | "required" | string
-  labels: MergeableMap
+  labels: MergeableMap_LabelConfig
     |:
       *: LabelConfig
         |: string
@@ -348,7 +360,7 @@ conversation: ConversationConfig
                   args?: [string]
                   program: string
                   shell?: bool
-    |: MergedMap
+    |: MergedMap_LabelConfig
       discard_when_merged?: bool
       strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
       value?:
@@ -411,12 +423,12 @@ conversation: ConversationConfig
     *: ToolsDefaultsConfig
       access:
         |: AccessConfig
-          env: MergeableVec
+          env: MergeableVec_EnvRuleConfig
             |:
               []: EnvRuleConfig
                 name: string
                 read: bool | null
-            |: MergedVec
+            |: MergedVec_EnvRuleConfig
               dedup?: "inherit" | "true" | "false" | bool | null
               discard_when_merged?: bool
               strategy?: "append" | "prepend" | "replace" | null
@@ -424,7 +436,7 @@ conversation: ConversationConfig
                 []: EnvRuleConfig
                   name: string
                   read: bool | null
-          fs: MergeableVec
+          fs: MergeableVec_FsRuleConfig
             |:
               []: FsRuleConfig
                 create: bool | null
@@ -435,7 +447,7 @@ conversation: ConversationConfig
                 read: bool | null
                 update: bool | null
                 write: bool | null
-            |: MergedVec
+            |: MergedVec_FsRuleConfig
               dedup?: "inherit" | "true" | "false" | bool | null
               discard_when_merged?: bool
               strategy?: "append" | "prepend" | "replace" | null
@@ -481,39 +493,26 @@ conversation: ConversationConfig
               shell?: bool
         print_stderr?: bool
         results_file_link?: "full" | "osc8" | "off"
-    tools (flattened):
-      *: ToolConfig
-        access:
-          |: AccessConfig
-            env: MergeableVec
-              |:
-                []: EnvRuleConfig
-                  name: string
-                  read: bool | null
-              |: MergedVec
-                dedup?: "inherit" | "true" | "false" | bool | null
-                discard_when_merged?: bool
-                strategy?: "append" | "prepend" | "replace" | null
-                value?:
+    tools (flattened): MergeableMap_ToolConfig
+      |:
+        *: ToolConfig
+          access:
+            |: AccessConfig
+              env: MergeableVec_EnvRuleConfig
+                |:
                   []: EnvRuleConfig
                     name: string
                     read: bool | null
-            fs: MergeableVec
-              |:
-                []: FsRuleConfig
-                  create: bool | null
-                  delete: bool | null
-                  execute: bool | null
-                  external: bool | null
-                  path: string
-                  read: bool | null
-                  update: bool | null
-                  write: bool | null
-              |: MergedVec
-                dedup?: "inherit" | "true" | "false" | bool | null
-                discard_when_merged?: bool
-                strategy?: "append" | "prepend" | "replace" | null
-                value?:
+                |: MergedVec_EnvRuleConfig
+                  dedup?: "inherit" | "true" | "false" | bool | null
+                  discard_when_merged?: bool
+                  strategy?: "append" | "prepend" | "replace" | null
+                  value?:
+                    []: EnvRuleConfig
+                      name: string
+                      read: bool | null
+              fs: MergeableVec_FsRuleConfig
+                |:
                   []: FsRuleConfig
                     create: bool | null
                     delete: bool | null
@@ -523,69 +522,84 @@ conversation: ConversationConfig
                     read: bool | null
                     update: bool | null
                     write: bool | null
-          |: null
-        cancellation_response: string | null
-        command:
-          |: CommandConfigOrString
-            |: string
-            | (expanded): CommandConfig
-              args?: [string]
-              program: string
-              shell?: bool
-          |: null
-        description: string | null
-        enable:
-          |:
-            |: bool
-            |: "on" | "off" | "always" | "explicit"
-            | (expanded): EnableConfig
-              allow_toggle: "any" | "never" | "if_named" | "if_named_or_group" | null
-              state: bool | null
-          |: null
-        examples: string | null
-        format: "ask" | "unattended" | null
-        options:
-          *: unknown
-        parameters:
-          *: ToolParameterConfig
-            default?: unknown | null
-            description?: string | null
-            enum?: [unknown] | null
-            examples?: string | null
-            items?: @ToolParameterConfig | null
-            properties?:
-              *: @ToolParameterConfig
-            required?: bool | null
-            summary?: string | null
-            type?: string | [string] | null
-        questions:
-          *: QuestionConfig
-            answer: unknown | null
-            target: QuestionTarget
-              |: "user" | "assistant"
-              |: PartialAssistantConfig
-                instructions?:
-                  |: PartialMergeableVec
-                    |:
-                      []: PartialInstructionsConfig
-                        description?: string | null
-                        examples?:
-                          |:
-                            []: PartialExampleConfig
-                              |: string
-                              |: PartialContrastConfig
-                                bad?: string | null
-                                good?: string | null
-                                reason?: string | null
-                          |: null
-                        items?: [string] | null
-                        position?: int | null
-                        title?: string | null
-                    |: PartialMergedVec
-                      dedup?: "inherit" | "true" | "false" | bool | null | null
-                      discard_when_merged?: bool | null
-                      strategy?: "append" | "prepend" | "replace" | null
-                      value?:
+                |: MergedVec_FsRuleConfig
+                  dedup?: "inherit" | "true" | "false" | bool | null
+                  discard_when_merged?: bool
+                  strategy?: "append" | "prepend" | "replace" | null
+                  value?:
+                    []: FsRuleConfig
+                      create: bool | null
+                      delete: bool | null
+                      execute: bool | null
+                      external: bool | null
+                      path: string
+                      read: bool | null
+                      update: bool | null
+                      write: bool | null
+            |: null
+          cancellation_response: string | null
+          command:
+            |: CommandConfigOrString
+              |: string
+              | (expanded): CommandConfig
+                args?: [string]
+                program: string
+                shell?: bool
+            |: null
+          description: string | null
+          enable:
+            |:
+              |: bool
+              |: "on" | "off" | "always" | "explicit"
+              | (expanded): EnableConfig
+                allow_toggle: "any" | "never" | "if_named" | "if_named_or_group" | null
+                state: bool | null
+            |: null
+          examples: string | null
+          format: "ask" | "unattended" | null
+          options: MergeableMap_JsonValue
+            |:
+              *: unknown
+            |: MergedMap_JsonValue
+              discard_when_merged?: bool
+              strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+              value?:
+                *: unknown
+          parameters: MergeableMap_ToolParameterConfig
+            |:
+              *: ToolParameterConfig
+                default?: unknown | null
+                description?: string | null
+                enum?: [unknown] | null
+                examples?: string | null
+                items?: @ToolParameterConfig | null
+                properties?: @MergeableMap_ToolParameterConfig
+                required?: bool | null
+                summary?: string | null
+                type?: string | [string] | null
+            |: MergedMap_ToolParameterConfig
+              discard_when_merged?: bool
+              strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+              value?:
+                *: ToolParameterConfig
+                  default?: unknown | null
+                  description?: string | null
+                  enum?: [unknown] | null
+                  examples?: string | null
+                  items?: @ToolParameterConfig | null
+                  properties?: @MergeableMap_ToolParameterConfig
+                  required?: bool | null
+                  summary?: string | null
+                  type?: string | [string] | null
+          questions: MergeableMap_QuestionConfig
+            |:
+              *: QuestionConfig
+                answer: unknown | null
+                target: QuestionTarget
+                  |: "user" | "assistant"
+                  |: PartialAssistantConfig
+                    instructions?:
+                      |: PartialMergeableVec_InstructionsConfig
                         |:
                           []: PartialInstructionsConfig
                             description?: string | null
@@ -601,114 +615,644 @@ conversation: ConversationConfig
                             items?: [string] | null
                             position?: int | null
                             title?: string | null
-                        |: null
-                  |: null
-                model?:
-                  |: PartialModelConfig
-                    id?:
-                      |: PartialModelIdOrAliasConfig
-                        |: PartialModelIdConfig
-                          name?: string | null
-                          provider?: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai" | null
-                        |: string
+                        |: PartialMergedVec_InstructionsConfig
+                          dedup?: "inherit" | "true" | "false" | bool | null | null
+                          discard_when_merged?: bool | null
+                          strategy?: "append" | "prepend" | "replace" | null
+                          value?:
+                            |:
+                              []: PartialInstructionsConfig
+                                description?: string | null
+                                examples?:
+                                  |:
+                                    []: PartialExampleConfig
+                                      |: string
+                                      |: PartialContrastConfig
+                                        bad?: string | null
+                                        good?: string | null
+                                        reason?: string | null
+                                  |: null
+                                items?: [string] | null
+                                position?: int | null
+                                title?: string | null
+                            |: null
                       |: null
-                    parameters?:
-                      |: PartialParametersConfig
-                        max_tokens?: int | null
-                        other?:
-                          |:
-                            *: unknown
+                    model?:
+                      |: PartialModelConfig
+                        id?:
+                          |: PartialModelIdOrAliasConfig
+                            |: PartialModelIdConfig
+                              name?: string | null
+                              provider?: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai" | null
+                            |: string
                           |: null
-                        reasoning?:
-                          |: PartialReasoningConfig
-                            |: "off"
-                            |: "auto"
-                            |: PartialCustomReasoningConfig
-                              effort?: "none" | "auto" | "max" | "xhigh" | "high" | "medium" | "low" | "xlow" | string | null
-                              exclude?: bool | null
-                          |: null
-                        service_tier?: "off" | "flex" | "standard" | "priority" | null
-                        stop_words?:
-                          |: MergeableVec
-                            |: [string]
-                            |: PartialMergedVec
-                              dedup?: "inherit" | "true" | "false" | bool | null | null
-                              discard_when_merged?: bool | null
-                              strategy?: "append" | "prepend" | "replace" | null
-                              value?: [string] | null
+                        parameters?:
+                          |: PartialParametersConfig
+                            max_tokens?: int | null
+                            other?:
+                              |:
+                                *: unknown
+                              |: null
+                            reasoning?:
+                              |: PartialReasoningConfig
+                                |: "off"
+                                |: "auto"
+                                |: PartialCustomReasoningConfig
+                                  effort?: "none" | "auto" | "max" | "xhigh" | "high" | "medium" | "low" | "xlow" | string | null
+                                  exclude?: bool | null
+                              |: null
+                            service_tier?: "off" | "flex" | "standard" | "priority" | null
+                            stop_words?:
+                              |: MergeableVec
+                                |: [string]
+                                |: PartialMergedVec
+                                  dedup?: "inherit" | "true" | "false" | bool | null | null
+                                  discard_when_merged?: bool | null
+                                  strategy?: "append" | "prepend" | "replace" | null
+                                  value?: [string] | null
+                              |: null
+                            temperature?: float | null
+                            top_k?: int | null
+                            top_p?: float | null
                           |: null
-                        temperature?: float | null
-                        top_k?: int | null
-                        top_p?: float | null
                       |: null
-                  |: null
-                name?: string | null
-                request?:
-                  |: PartialRequestConfig
-                    base_backoff_ms?: int | null
-                    cache?: bool | "off" | "short" | "long" | string | null
-                    max_backoff_secs?: int | null
-                    max_response_bytes?: int | "disabled" | "off" | bool | null
-                    max_retries?: int | null
-                    stream_idle_timeout_secs?: int | null
-                  |: null
-                system_prompt?:
-                  |: PartialMergeableString
-                    |: string
-                    |: PartialMergedString
-                      dedup?: bool | "inherit" | "off" | "exact" | "block" | "contains" | null | null
-                      discard_when_merged?: bool | null
-                      separator?: "none" | "space" | "line" | "paragraph" | null
-                      strategy?: "append" | "prepend" | "replace" | null
-                      value?: string | null
-                  |: null
-                system_prompt_sections?:
-                  |: PartialMergeableVec
-                    |:
-                      []: PartialSectionConfig
-                        content?: string | null
-                        position?: int | null
-                        tag?: string | null
-                        title?: string | null
-                    |: PartialMergedVec
-                      dedup?: "inherit" | "true" | "false" | bool | null | null
-                      discard_when_merged?: bool | null
-                      strategy?: "append" | "prepend" | "replace" | null
-                      value?:
+                    name?: string | null
+                    request?:
+                      |: PartialRequestConfig
+                        base_backoff_ms?: int | null
+                        cache?: bool | "off" | "short" | "long" | string | null
+                        max_backoff_secs?: int | null
+                        max_response_bytes?: int | "disabled" | "off" | bool | null
+                        max_retries?: int | null
+                        stream_idle_timeout_secs?: int | null
+                      |: null
+                    system_prompt?:
+                      |: PartialMergeableString
+                        |: string
+                        |: PartialMergedString
+                          dedup?: bool | "inherit" | "off" | "exact" | "block" | "contains" | null | null
+                          discard_when_merged?: bool | null
+                          separator?: "none" | "space" | "line" | "paragraph" | null
+                          strategy?: "append" | "prepend" | "replace" | null
+                          value?: string | null
+                      |: null
+                    system_prompt_sections?:
+                      |: PartialMergeableVec_SectionConfig
                         |:
                           []: PartialSectionConfig
                             content?: string | null
                             position?: int | null
                             tag?: string | null
                             title?: string | null
+                        |: PartialMergedVec_SectionConfig
+                          dedup?: "inherit" | "true" | "false" | bool | null | null
+                          discard_when_merged?: bool | null
+                          strategy?: "append" | "prepend" | "replace" | null
+                          value?:
+                            |:
+                              []: PartialSectionConfig
+                                content?: string | null
+                                position?: int | null
+                                tag?: string | null
+                                title?: string | null
+                            |: null
+                      |: null
+                    tool_choice?: "auto" | "none" | "required" | string | null
+            |: MergedMap_QuestionConfig
+              discard_when_merged?: bool
+              strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+              value?:
+                *: QuestionConfig
+                  answer: unknown | null
+                  target: QuestionTarget
+                    |: "user" | "assistant"
+                    |: PartialAssistantConfig
+                      instructions?:
+                        |: PartialMergeableVec_InstructionsConfig
+                          |:
+                            []: PartialInstructionsConfig
+                              description?: string | null
+                              examples?:
+                                |:
+                                  []: PartialExampleConfig
+                                    |: string
+                                    |: PartialContrastConfig
+                                      bad?: string | null
+                                      good?: string | null
+                                      reason?: string | null
+                                |: null
+                              items?: [string] | null
+                              position?: int | null
+                              title?: string | null
+                          |: PartialMergedVec_InstructionsConfig
+                            dedup?: "inherit" | "true" | "false" | bool | null | null
+                            discard_when_merged?: bool | null
+                            strategy?: "append" | "prepend" | "replace" | null
+                            value?:
+                              |:
+                                []: PartialInstructionsConfig
+                                  description?: string | null
+                                  examples?:
+                                    |:
+                                      []: PartialExampleConfig
+                                        |: string
+                                        |: PartialContrastConfig
+                                          bad?: string | null
+                                          good?: string | null
+                                          reason?: string | null
+                                    |: null
+                                  items?: [string] | null
+                                  position?: int | null
+                                  title?: string | null
+                              |: null
                         |: null
-                  |: null
-                tool_choice?: "auto" | "none" | "required" | string | null
-        result: "unattended" | "ask" | "edit" | "skip" | null
-        run: "ask" | "unattended" | "edit" | "skip" | null
-        source: string(/^(builtin|local)(\..+)?$|^mcp\.[^.]+(\..+)?$/)
-        style:
-          |: DisplayStyleConfig
-            error: ErrorStyleConfig
-              inline_results: "off" | "full" | string | null
-              results_file_link: "full" | "osc8" | "off" | null
-            hidden?: bool
-            inline_results?: "off" | "full" | string
-            joins_reasoning?: bool
-            parameters?: ParametersStyle
-              |: "json"
-              |: "function_call"
-              |: "off"
+                      model?:
+                        |: PartialModelConfig
+                          id?:
+                            |: PartialModelIdOrAliasConfig
+                              |: PartialModelIdConfig
+                                name?: string | null
+                                provider?: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai" | null
+                              |: string
+                            |: null
+                          parameters?:
+                            |: PartialParametersConfig
+                              max_tokens?: int | null
+                              other?:
+                                |:
+                                  *: unknown
+                                |: null
+                              reasoning?:
+                                |: PartialReasoningConfig
+                                  |: "off"
+                                  |: "auto"
+                                  |: PartialCustomReasoningConfig
+                                    effort?: "none" | "auto" | "max" | "xhigh" | "high" | "medium" | "low" | "xlow" | string | null
+                                    exclude?: bool | null
+                                |: null
+                              service_tier?: "off" | "flex" | "standard" | "priority" | null
+                              stop_words?:
+                                |: MergeableVec
+                                  |: [string]
+                                  |: PartialMergedVec
+                                    dedup?: "inherit" | "true" | "false" | bool | null | null
+                                    discard_when_merged?: bool | null
+                                    strategy?: "append" | "prepend" | "replace" | null
+                                    value?: [string] | null
+                                |: null
+                              temperature?: float | null
+                              top_k?: int | null
+                              top_p?: float | null
+                            |: null
+                        |: null
+                      name?: string | null
+                      request?:
+                        |: PartialRequestConfig
+                          base_backoff_ms?: int | null
+                          cache?: bool | "off" | "short" | "long" | string | null
+                          max_backoff_secs?: int | null
+                          max_response_bytes?: int | "disabled" | "off" | bool | null
+                          max_retries?: int | null
+                          stream_idle_timeout_secs?: int | null
+                        |: null
+                      system_prompt?:
+                        |: PartialMergeableString
+                          |: string
+                          |: PartialMergedString
+                            dedup?: bool | "inherit" | "off" | "exact" | "block" | "contains" | null | null
+                            discard_when_merged?: bool | null
+                            separator?: "none" | "space" | "line" | "paragraph" | null
+                            strategy?: "append" | "prepend" | "replace" | null
+                            value?: string | null
+                        |: null
+                      system_prompt_sections?:
+                        |: PartialMergeableVec_SectionConfig
+                          |:
+                            []: PartialSectionConfig
+                              content?: string | null
+                              position?: int | null
+                              tag?: string | null
+                              title?: string | null
+                          |: PartialMergedVec_SectionConfig
+                            dedup?: "inherit" | "true" | "false" | bool | null | null
+                            discard_when_merged?: bool | null
+                            strategy?: "append" | "prepend" | "replace" | null
+                            value?:
+                              |:
+                                []: PartialSectionConfig
+                                  content?: string | null
+                                  position?: int | null
+                                  tag?: string | null
+                                  title?: string | null
+                              |: null
+                        |: null
+                      tool_choice?: "auto" | "none" | "required" | string | null
+          result: "unattended" | "ask" | "edit" | "skip" | null
+          run: "ask" | "unattended" | "edit" | "skip" | null
+          source: string(/^(builtin|local)(\..+)?$|^mcp\.[^.]+(\..+)?$/)
+          style:
+            |: DisplayStyleConfig
+              error: ErrorStyleConfig
+                inline_results: "off" | "full" | string | null
+                results_file_link: "full" | "osc8" | "off" | null
+              hidden?: bool
+              inline_results?: "off" | "full" | string
+              joins_reasoning?: bool
+              parameters?: ParametersStyle
+                |: "json"
+                |: "function_call"
+                |: "off"
+                |: CommandConfigOrString
+                  |: string
+                  | (expanded): CommandConfig
+                    args?: [string]
+                    program: string
+                    shell?: bool
+              print_stderr?: bool
+              results_file_link?: "full" | "osc8" | "off"
+            |: null
+          summary: string | null
+      |: MergedMap_ToolConfig
+        discard_when_merged?: bool
+        strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+        value?:
+          *: ToolConfig
+            access:
+              |: AccessConfig
+                env: MergeableVec_EnvRuleConfig
+                  |:
+                    []: EnvRuleConfig
+                      name: string
+                      read: bool | null
+                  |: MergedVec_EnvRuleConfig
+                    dedup?: "inherit" | "true" | "false" | bool | null
+                    discard_when_merged?: bool
+                    strategy?: "append" | "prepend" | "replace" | null
+                    value?:
+                      []: EnvRuleConfig
+                        name: string
+                        read: bool | null
+                fs: MergeableVec_FsRuleConfig
+                  |:
+                    []: FsRuleConfig
+                      create: bool | null
+                      delete: bool | null
+                      execute: bool | null
+                      external: bool | null
+                      path: string
+                      read: bool | null
+                      update: bool | null
+                      write: bool | null
+                  |: MergedVec_FsRuleConfig
+                    dedup?: "inherit" | "true" | "false" | bool | null
+                    discard_when_merged?: bool
+                    strategy?: "append" | "prepend" | "replace" | null
+                    value?:
+                      []: FsRuleConfig
+                        create: bool | null
+                        delete: bool | null
+                        execute: bool | null
+                        external: bool | null
+                        path: string
+                        read: bool | null
+                        update: bool | null
+                        write: bool | null
+              |: null
+            cancellation_response: string | null
+            command:
               |: CommandConfigOrString
                 |: string
                 | (expanded): CommandConfig
                   args?: [string]
                   program: string
                   shell?: bool
-            print_stderr?: bool
-            results_file_link?: "full" | "osc8" | "off"
-          |: null
-        summary: string | null
+              |: null
+            description: string | null
+            enable:
+              |:
+                |: bool
+                |: "on" | "off" | "always" | "explicit"
+                | (expanded): EnableConfig
+                  allow_toggle: "any" | "never" | "if_named" | "if_named_or_group" | null
+                  state: bool | null
+              |: null
+            examples: string | null
+            format: "ask" | "unattended" | null
+            options: MergeableMap_JsonValue
+              |:
+                *: unknown
+              |: MergedMap_JsonValue
+                discard_when_merged?: bool
+                strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+                value?:
+                  *: unknown
+            parameters: MergeableMap_ToolParameterConfig
+              |:
+                *: ToolParameterConfig
+                  default?: unknown | null
+                  description?: string | null
+                  enum?: [unknown] | null
+                  examples?: string | null
+                  items?: @ToolParameterConfig | null
+                  properties?: @MergeableMap_ToolParameterConfig
+                  required?: bool | null
+                  summary?: string | null
+                  type?: string | [string] | null
+              |: MergedMap_ToolParameterConfig
+                discard_when_merged?: bool
+                strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+                value?:
+                  *: ToolParameterConfig
+                    default?: unknown | null
+                    description?: string | null
+                    enum?: [unknown] | null
+                    examples?: string | null
+                    items?: @ToolParameterConfig | null
+                    properties?: @MergeableMap_ToolParameterConfig
+                    required?: bool | null
+                    summary?: string | null
+                    type?: string | [string] | null
+            questions: MergeableMap_QuestionConfig
+              |:
+                *: QuestionConfig
+                  answer: unknown | null
+                  target: QuestionTarget
+                    |: "user" | "assistant"
+                    |: PartialAssistantConfig
+                      instructions?:
+                        |: PartialMergeableVec_InstructionsConfig
+                          |:
+                            []: PartialInstructionsConfig
+                              description?: string | null
+                              examples?:
+                                |:
+                                  []: PartialExampleConfig
+                                    |: string
+                                    |: PartialContrastConfig
+                                      bad?: string | null
+                                      good?: string | null
+                                      reason?: string | null
+                                |: null
+                              items?: [string] | null
+                              position?: int | null
+                              title?: string | null
+                          |: PartialMergedVec_InstructionsConfig
+                            dedup?: "inherit" | "true" | "false" | bool | null | null
+                            discard_when_merged?: bool | null
+                            strategy?: "append" | "prepend" | "replace" | null
+                            value?:
+                              |:
+                                []: PartialInstructionsConfig
+                                  description?: string | null
+                                  examples?:
+                                    |:
+                                      []: PartialExampleConfig
+                                        |: string
+                                        |: PartialContrastConfig
+                                          bad?: string | null
+                                          good?: string | null
+                                          reason?: string | null
+                                    |: null
+                                  items?: [string] | null
+                                  position?: int | null
+                                  title?: string | null
+                              |: null
+                        |: null
+                      model?:
+                        |: PartialModelConfig
+                          id?:
+                            |: PartialModelIdOrAliasConfig
+                              |: PartialModelIdConfig
+                                name?: string | null
+                                provider?: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai" | null
+                              |: string
+                            |: null
+                          parameters?:
+                            |: PartialParametersConfig
+                              max_tokens?: int | null
+                              other?:
+                                |:
+                                  *: unknown
+                                |: null
+                              reasoning?:
+                                |: PartialReasoningConfig
+                                  |: "off"
+                                  |: "auto"
+                                  |: PartialCustomReasoningConfig
+                                    effort?: "none" | "auto" | "max" | "xhigh" | "high" | "medium" | "low" | "xlow" | string | null
+                                    exclude?: bool | null
+                                |: null
+                              service_tier?: "off" | "flex" | "standard" | "priority" | null
+                              stop_words?:
+                                |: MergeableVec
+                                  |: [string]
+                                  |: PartialMergedVec
+                                    dedup?: "inherit" | "true" | "false" | bool | null | null
+                                    discard_when_merged?: bool | null
+                                    strategy?: "append" | "prepend" | "replace" | null
+                                    value?: [string] | null
+                                |: null
+                              temperature?: float | null
+                              top_k?: int | null
+                              top_p?: float | null
+                            |: null
+                        |: null
+                      name?: string | null
+                      request?:
+                        |: PartialRequestConfig
+                          base_backoff_ms?: int | null
+                          cache?: bool | "off" | "short" | "long" | string | null
+                          max_backoff_secs?: int | null
+                          max_response_bytes?: int | "disabled" | "off" | bool | null
+                          max_retries?: int | null
+                          stream_idle_timeout_secs?: int | null
+                        |: null
+                      system_prompt?:
+                        |: PartialMergeableString
+                          |: string
+                          |: PartialMergedString
+                            dedup?: bool | "inherit" | "off" | "exact" | "block" | "contains" | null | null
+                            discard_when_merged?: bool | null
+                            separator?: "none" | "space" | "line" | "paragraph" | null
+                            strategy?: "append" | "prepend" | "replace" | null
+                            value?: string | null
+                        |: null
+                      system_prompt_sections?:
+                        |: PartialMergeableVec_SectionConfig
+                          |:
+                            []: PartialSectionConfig
+                              content?: string | null
+                              position?: int | null
+                              tag?: string | null
+                              title?: string | null
+                          |: PartialMergedVec_SectionConfig
+                            dedup?: "inherit" | "true" | "false" | bool | null | null
+                            discard_when_merged?: bool | null
+                            strategy?: "append" | "prepend" | "replace" | null
+                            value?:
+                              |:
+                                []: PartialSectionConfig
+                                  content?: string | null
+                                  position?: int | null
+                                  tag?: string | null
+                                  title?: string | null
+                              |: null
+                        |: null
+                      tool_choice?: "auto" | "none" | "required" | string | null
+              |: MergedMap_QuestionConfig
+                discard_when_merged?: bool
+                strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+                value?:
+                  *: QuestionConfig
+                    answer: unknown | null
+                    target: QuestionTarget
+                      |: "user" | "assistant"
+                      |: PartialAssistantConfig
+                        instructions?:
+                          |: PartialMergeableVec_InstructionsConfig
+                            |:
+                              []: PartialInstructionsConfig
+                                description?: string | null
+                                examples?:
+                                  |:
+                                    []: PartialExampleConfig
+                                      |: string
+                                      |: PartialContrastConfig
+                                        bad?: string | null
+                                        good?: string | null
+                                        reason?: string | null
+                                  |: null
+                                items?: [string] | null
+                                position?: int | null
+                                title?: string | null
+                            |: PartialMergedVec_InstructionsConfig
+                              dedup?: "inherit" | "true" | "false" | bool | null | null
+                              discard_when_merged?: bool | null
+                              strategy?: "append" | "prepend" | "replace" | null
+                              value?:
+                                |:
+                                  []: PartialInstructionsConfig
+                                    description?: string | null
+                                    examples?:
+                                      |:
+                                        []: PartialExampleConfig
+                                          |: string
+                                          |: PartialContrastConfig
+                                            bad?: string | null
+                                            good?: string | null
+                                            reason?: string | null
+                                      |: null
+                                    items?: [string] | null
+                                    position?: int | null
+                                    title?: string | null
+                                |: null
+                          |: null
+                        model?:
+                          |: PartialModelConfig
+                            id?:
+                              |: PartialModelIdOrAliasConfig
+                                |: PartialModelIdConfig
+                                  name?: string | null
+                                  provider?: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai" | null
+                                |: string
+                              |: null
+                            parameters?:
+                              |: PartialParametersConfig
+                                max_tokens?: int | null
+                                other?:
+                                  |:
+                                    *: unknown
+                                  |: null
+                                reasoning?:
+                                  |: PartialReasoningConfig
+                                    |: "off"
+                                    |: "auto"
+                                    |: PartialCustomReasoningConfig
+                                      effort?: "none" | "auto" | "max" | "xhigh" | "high" | "medium" | "low" | "xlow" | string | null
+                                      exclude?: bool | null
+                                  |: null
+                                service_tier?: "off" | "flex" | "standard" | "priority" | null
+                                stop_words?:
+                                  |: MergeableVec
+                                    |: [string]
+                                    |: PartialMergedVec
+                                      dedup?: "inherit" | "true" | "false" | bool | null | null
+                                      discard_when_merged?: bool | null
+                                      strategy?: "append" | "prepend" | "replace" | null
+                                      value?: [string] | null
+                                  |: null
+                                temperature?: float | null
+                                top_k?: int | null
+                                top_p?: float | null
+                              |: null
+                          |: null
+                        name?: string | null
+                        request?:
+                          |: PartialRequestConfig
+                            base_backoff_ms?: int | null
+                            cache?: bool | "off" | "short" | "long" | string | null
+                            max_backoff_secs?: int | null
+                            max_response_bytes?: int | "disabled" | "off" | bool | null
+                            max_retries?: int | null
+                            stream_idle_timeout_secs?: int | null
+                          |: null
+                        system_prompt?:
+                          |: PartialMergeableString
+                            |: string
+                            |: PartialMergedString
+                              dedup?: bool | "inherit" | "off" | "exact" | "block" | "contains" | null | null
+                              discard_when_merged?: bool | null
+                              separator?: "none" | "space" | "line" | "paragraph" | null
+                              strategy?: "append" | "prepend" | "replace" | null
+                              value?: string | null
+                          |: null
+                        system_prompt_sections?:
+                          |: PartialMergeableVec_SectionConfig
+                            |:
+                              []: PartialSectionConfig
+                                content?: string | null
+                                position?: int | null
+                                tag?: string | null
+                                title?: string | null
+                            |: PartialMergedVec_SectionConfig
+                              dedup?: "inherit" | "true" | "false" | bool | null | null
+                              discard_when_merged?: bool | null
+                              strategy?: "append" | "prepend" | "replace" | null
+                              value?:
+                                |:
+                                  []: PartialSectionConfig
+                                    content?: string | null
+                                    position?: int | null
+                                    tag?: string | null
+                                    title?: string | null
+                                |: null
+                          |: null
+                        tool_choice?: "auto" | "none" | "required" | string | null
+            result: "unattended" | "ask" | "edit" | "skip" | null
+            run: "ask" | "unattended" | "edit" | "skip" | null
+            source: string(/^(builtin|local)(\..+)?$|^mcp\.[^.]+(\..+)?$/)
+            style:
+              |: DisplayStyleConfig
+                error: ErrorStyleConfig
+                  inline_results: "off" | "full" | string | null
+                  results_file_link: "full" | "osc8" | "off" | null
+                hidden?: bool
+                inline_results?: "off" | "full" | string
+                joins_reasoning?: bool
+                parameters?: ParametersStyle
+                  |: "json"
+                  |: "function_call"
+                  |: "off"
+                  |: CommandConfigOrString
+                    |: string
+                    | (expanded): CommandConfig
+                      args?: [string]
+                      program: string
+                      shell?: bool
+                print_stderr?: bool
+                results_file_link?: "full" | "osc8" | "off"
+              |: null
+            summary: string | null
 editor: EditorConfig
   cmd:
     |: CommandConfigOrString
@@ -746,25 +1290,49 @@ loader: LoaderConfig
   reset: "none" | null
 plugins: PluginsConfig
   auto_install?: bool
-  command:
-    *: CommandPluginConfig
-      checksum:
-        |: ChecksumConfig
-          algorithm?: "sha256" | "sha1"
-          value: string
-        |: null
-      install: bool | null
-      options: unknown | null
-      run: "ask" | "unattended" | "deny" | null
+  command: MergeableMap_CommandPluginConfig
+    |:
+      *: CommandPluginConfig
+        checksum:
+          |: ChecksumConfig
+            algorithm?: "sha256" | "sha1"
+            value: string
+          |: null
+        install: bool | null
+        options: unknown | null
+        run: "ask" | "unattended" | "deny" | null
+    |: MergedMap_CommandPluginConfig
+      discard_when_merged?: bool
+      strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+      value?:
+        *: CommandPluginConfig
+          checksum:
+            |: ChecksumConfig
+              algorithm?: "sha256" | "sha1"
+              value: string
+            |: null
+          install: bool | null
+          options: unknown | null
+          run: "ask" | "unattended" | "deny" | null
   shutdown_timeout_secs?: int
 providers: ProviderConfig
   llm: LlmProviderConfig
-    aliases:
-      *: ModelIdOrAliasConfig
-        |: ModelIdConfig
-          name: string
-          provider: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai"
-        |: string
+    aliases: MergeableMap_ModelIdOrAliasConfig
+      |:
+        *: ModelIdOrAliasConfig
+          |: ModelIdConfig
+            name: string
+            provider: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai"
+          |: string
+      |: MergedMap_ModelIdOrAliasConfig
+        discard_when_merged?: bool
+        strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+        value?:
+          *: ModelIdOrAliasConfig
+            |: ModelIdConfig
+              name: string
+              provider: "anthropic" | "cerebras" | "deepseek" | "google" | "llamacpp" | "ollama" | "openai" | "openrouter" | "xai"
+            |: string
     anthropic: AnthropicConfig
       api_key_env?: string
       auth?: [string]
@@ -799,32 +1367,62 @@ providers: ProviderConfig
       app_name?: string
       app_referrer: string | null
       base_url?: string
-  mcp:
-    *: McpProviderConfig
-      |: StdioConfig
-        arguments?: MergeableVec
-          |: [string]
-          |: MergedVec
-            dedup?: "inherit" | "true" | "false" | bool | null
-            discard_when_merged?: bool
-            strategy?: "append" | "prepend" | "replace" | null
-            value?: [string]
-        checksum:
-          |: ChecksumConfig
-            algorithm?: "sha256" | "sha1"
-            value: string
-          |: null
-        command: string
-        optional?: bool
-        startup_timeout_secs?: int
-        type: "stdio"
-        variables?: MergeableVec
-          |: [string]
-          |: MergedVec
-            dedup?: "inherit" | "true" | "false" | bool | null
-            discard_when_merged?: bool
-            strategy?: "append" | "prepend" | "replace" | null
-            value?: [string]
+  mcp: MergeableMap_McpProviderConfig
+    |:
+      *: McpProviderConfig
+        |: StdioConfig
+          arguments?: MergeableVec
+            |: [string]
+            |: MergedVec
+              dedup?: "inherit" | "true" | "false" | bool | null
+              discard_when_merged?: bool
+              strategy?: "append" | "prepend" | "replace" | null
+              value?: [string]
+          checksum:
+            |: ChecksumConfig
+              algorithm?: "sha256" | "sha1"
+              value: string
+            |: null
+          command: string
+          optional?: bool
+          startup_timeout_secs?: int
+          type: "stdio"
+          variables?: MergeableVec
+            |: [string]
+            |: MergedVec
+              dedup?: "inherit" | "true" | "false" | bool | null
+              discard_when_merged?: bool
+              strategy?: "append" | "prepend" | "replace" | null
+              value?: [string]
+    |: MergedMap_McpProviderConfig
+      discard_when_merged?: bool
+      strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+      value?:
+        *: McpProviderConfig
+          |: StdioConfig
+            arguments?: MergeableVec
+              |: [string]
+              |: MergedVec
+                dedup?: "inherit" | "true" | "false" | bool | null
+                discard_when_merged?: bool
+                strategy?: "append" | "prepend" | "replace" | null
+                value?: [string]
+            checksum:
+              |: ChecksumConfig
+                algorithm?: "sha256" | "sha1"
+                value: string
+              |: null
+            command: string
+            optional?: bool
+            startup_timeout_secs?: int
+            type: "stdio"
+            variables?: MergeableVec
+              |: [string]
+              |: MergedVec
+                dedup?: "inherit" | "true" | "false" | bool | null
+                discard_when_merged?: bool
+                strategy?: "append" | "prepend" | "replace" | null
+                value?: [string]
 style: StyleConfig
   code: CodeConfig
     color?: bool
@@ -898,7 +1496,13 @@ style: StyleConfig
     max_latency?: string
     text_delay?: string
 template: TemplateConfig
-  values:
-    *: unknown
+  values: MergeableMap_JsonValue
+    |:
+      *: unknown
+    |: MergedMap_JsonValue
+      discard_when_merged?: bool
+      strategy?: "deep_merge" | "merge" | "keep" | "replace" | null
+      value?:
+        *: unknown
 user: UserConfig
   name: string | null
diff --git a/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default.snap b/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default.snap
index 16521dbf1..19597f429 100644
--- a/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default.snap
+++ b/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default.snap
@@ -75,7 +75,9 @@ PartialAppConfig {
                 },
                 access: None,
             },
-            tools: {},
+            tools: Map(
+                {},
+            ),
         },
         compaction: PartialCompactionConfig {
             rules: Vec(
@@ -211,11 +213,15 @@ PartialAppConfig {
         },
     },
     template: PartialTemplateConfig {
-        values: {},
+        values: Map(
+            {},
+        ),
     },
     providers: PartialProviderConfig {
         llm: PartialLlmProviderConfig {
-            aliases: {},
+            aliases: Map(
+                {},
+            ),
             anthropic: PartialAnthropicConfig {
                 auth: None,
                 api_key_env: None,
@@ -253,12 +259,16 @@ PartialAppConfig {
                 base_url: None,
             },
         },
-        mcp: {},
+        mcp: Map(
+            {},
+        ),
     },
     plugins: PartialPluginsConfig {
         auto_install: None,
         shutdown_timeout_secs: None,
-        command: {},
+        command: Map(
+            {},
+        ),
     },
     user: PartialUserConfig {
         name: None,
diff --git a/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default_values.snap b/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default_values.snap
index 014fb57ad..cad679453 100644
--- a/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default_values.snap
+++ b/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_default_values.snap
@@ -144,7 +144,9 @@ Ok(
                         },
                         access: None,
                     },
-                    tools: {},
+                    tools: Map(
+                        {},
+                    ),
                 },
                 compaction: PartialCompactionConfig {
                     rules: Merged(
@@ -441,11 +443,15 @@ Ok(
                 },
             },
             template: PartialTemplateConfig {
-                values: {},
+                values: Map(
+                    {},
+                ),
             },
             providers: PartialProviderConfig {
                 llm: PartialLlmProviderConfig {
-                    aliases: {},
+                    aliases: Map(
+                        {},
+                    ),
                     anthropic: PartialAnthropicConfig {
                         auth: Some(
                             [
@@ -525,7 +531,9 @@ Ok(
                         ),
                     },
                 },
-                mcp: {},
+                mcp: Map(
+                    {},
+                ),
             },
             plugins: PartialPluginsConfig {
                 auto_install: Some(
@@ -534,7 +542,9 @@ Ok(
                 shutdown_timeout_secs: Some(
                     5,
                 ),
-                command: {},
+                command: Map(
+                    {},
+                ),
             },
             user: PartialUserConfig {
                 name: None,
diff --git a/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_empty_serialize.snap b/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_empty_serialize.snap
index a9220c267..0cb53742a 100644
--- a/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_empty_serialize.snap
+++ b/crates/jp_config/src/snapshots/jp_config__tests__partial_app_config_empty_serialize.snap
@@ -75,7 +75,9 @@ PartialAppConfig {
                 },
                 access: None,
             },
-            tools: {},
+            tools: Map(
+                {},
+            ),
         },
         compaction: PartialCompactionConfig {
             rules: Vec(
@@ -211,11 +213,15 @@ PartialAppConfig {
         },
     },
     template: PartialTemplateConfig {
-        values: {},
+        values: Map(
+            {},
+        ),
     },
     providers: PartialProviderConfig {
         llm: PartialLlmProviderConfig {
-            aliases: {},
+            aliases: Map(
+                {},
+            ),
             anthropic: PartialAnthropicConfig {
                 auth: None,
                 api_key_env: None,
@@ -253,12 +259,16 @@ PartialAppConfig {
                 base_url: None,
             },
         },
-        mcp: {},
+        mcp: Map(
+            {},
+        ),
     },
     plugins: PartialPluginsConfig {
         auto_install: None,
         shutdown_timeout_secs: None,
-        command: {},
+        command: Map(
+            {},
+        ),
     },
     user: PartialUserConfig {
         name: None,
diff --git a/crates/jp_config/src/template.rs b/crates/jp_config/src/template.rs
index 8174269c5..206a4c00f 100644
--- a/crates/jp_config/src/template.rs
+++ b/crates/jp_config/src/template.rs
@@ -1,15 +1,14 @@
 //! Template configuration for Jean-Pierre.
 
-use indexmap::IndexMap;
 use schematic::Config;
 
 use crate::{
     assignment::{AssignKeyValue, KvAssignment, missing_key},
-    delta::PartialConfigDelta,
+    delta::{PartialConfigDelta, delta_mergeable_value_map, delta_mergeable_value_map_at, path},
     fill::FillDefaults,
+    internal::merge::map_with_strategy,
     partial::ToPartial,
-    types::json_value::JsonValue,
-    util::merge_nested_indexmap,
+    types::{json_value::JsonValue, map::MergeableMap},
 };
 
 /// Template configuration.
@@ -17,15 +16,20 @@ use crate::{
 #[config(rename_all = "snake_case")]
 pub struct TemplateConfig {
     /// Template variable values used to render query templates.
-    #[setting(nested, merge = merge_nested_indexmap)]
-    pub values: IndexMap<String, JsonValue>,
+    ///
+    /// Entries merge by key, so a value set in a later layer joins the ones an
+    /// earlier layer set.
+    /// Declare the map as `{ value = { … }, strategy = "replace" }` to drop
+    /// them instead.
+    #[setting(nested, merge = map_with_strategy)]
+    pub values: MergeableMap<JsonValue>,
 }
 
 impl AssignKeyValue for PartialTemplateConfig {
     fn assign(&mut self, mut kv: KvAssignment) -> Result<(), crate::BoxedError> {
         match kv.key_string().as_str() {
             "" => kv.try_merge_object(self)?,
-            _ if kv.p("values") => kv.assign_to_entry(&mut self.values)?,
+            _ if kv.p("values") => kv.assign_to_mergeable_entry(&mut self.values)?,
             _ => return missing_key(&kv),
         }
 
@@ -36,34 +40,41 @@ impl AssignKeyValue for PartialTemplateConfig {
 impl PartialConfigDelta for PartialTemplateConfig {
     fn delta(&self, next: Self) -> Self {
         Self {
-            values: next
-                .values
-                .into_iter()
-                .filter_map(|(name, next)| {
-                    if self.values.get(&name).is_some_and(|prev| prev == &next) {
-                        return None;
-                    }
-                    Some((name, next))
-                })
-                .collect(),
+            values: delta_mergeable_value_map(&self.values, next.values),
+        }
+    }
+
+    fn delta_with_unsets(&self, next: Self, prefix: &str, unsets: &mut Vec<String>) -> Self {
+        Self {
+            values: delta_mergeable_value_map_at(
+                &path(prefix, "values"),
+                &self.values,
+                next.values,
+                unsets,
+            ),
         }
     }
 }
 
 impl FillDefaults for PartialTemplateConfig {
-    fn fill_from(self, _defaults: Self) -> Self {
-        self
+    fn fill_from(self, defaults: Self) -> Self {
+        Self {
+            values: self.values.fill_from(defaults.values),
+        }
     }
 }
 
 impl ToPartial for TemplateConfig {
     fn to_partial(&self) -> Self::Partial {
         Self::Partial {
-            values: self
-                .values
-                .iter()
-                .map(|(k, v)| (k.clone(), v.clone()))
-                .collect(),
+            // Per key rather than `replace`: a value the workspace config
+            // gained after this conversation was created still reaches it.
+            values: MergeableMap::Map(
+                self.values
+                    .iter()
+                    .map(|(k, v)| (k.clone(), v.clone()))
+                    .collect(),
+            ),
         }
     }
 }
diff --git a/crates/jp_config/src/types/map.rs b/crates/jp_config/src/types/map.rs
index 8553db23f..6d381eafa 100644
--- a/crates/jp_config/src/types/map.rs
+++ b/crates/jp_config/src/types/map.rs
@@ -64,22 +64,25 @@ where
     where
         D: Deserializer<'de>,
     {
-        // Try as `MergedMap` first (has `value` + `strategy` keys), then
-        // fall back to a plain map.
+        // Both variants are maps, so the keys decide which one this is: a table
+        // carrying `value` and `strategy` is the wrapper, anything else is a
+        // plain map. An entry named `value` alone is still an entry.
         UntaggedEnumVisitor::new()
             .map(|map| {
                 let value: serde_json::Value = map.deserialize()?;
 
-                // Peek: does this look like a MergedMap?
                 if let Some(obj) = value.as_object()
                     && obj.contains_key("value")
                     && obj.contains_key("strategy")
-                    && let Ok(merged) = serde_json::from_value::<MergedMap<T>>(value.clone())
                 {
-                    return Ok(Self::Merged(merged));
+                    // Committed: a malformed wrapper is an error rather than a
+                    // map that happens to use these two names, so a misspelled
+                    // strategy is reported instead of becoming an entry.
+                    return serde_json::from_value::<MergedMap<T>>(value)
+                        .map(Self::Merged)
+                        .map_err(serde::de::Error::custom);
                 }
 
-                // Plain map.
                 serde_json::from_value(value)
                     .map(Self::Map)
                     .map_err(serde::de::Error::custom)
@@ -182,6 +185,23 @@ pub fn map_to_mergeable_partial<'a, T: ToPartial + 'a>(
     })
 }
 
+/// Convert a resolved map to a `MergeableMap<T::Partial>` that merges per key.
+///
+/// Used by `ToPartial` impls for a map that should still take an entry a later
+/// layer adds, which a `replace` strategy would drop.
+/// Re-merging the result over the layer it came from reproduces it rather than
+/// combining with it, because each entry's own fields state their strategies.
+pub fn map_to_partial_per_key<'a, T: ToPartial + 'a>(
+    entries: impl IntoIterator<Item = (&'a String, &'a T)>,
+) -> MergeableMap<T::Partial> {
+    MergeableMap::Map(
+        entries
+            .into_iter()
+            .map(|(k, v)| (k.clone(), v.to_partial()))
+            .collect(),
+    )
+}
+
 impl<T> From<IndexMap<String, T>> for MergeableMap<T> {
     fn from(value: IndexMap<String, T>) -> Self {
         Self::Map(value)
diff --git a/crates/jp_config/src/types/map_tests.rs b/crates/jp_config/src/types/map_tests.rs
index d6999b382..b21ffee9a 100644
--- a/crates/jp_config/src/types/map_tests.rs
+++ b/crates/jp_config/src/types/map_tests.rs
@@ -2,6 +2,39 @@ use serde_json::json;
 
 use super::*;
 
+/// A schema names each type it expands and refers back to that name below, so
+/// two instantiations of one generic have to answer differently.
+///
+/// Sharing a name makes a consumer that resolves a reference walk a value
+/// against whichever instantiation it met first: a tool's `parameters` read as
+/// the map of tools, whose entries are a different type entirely.
+#[test]
+fn a_generic_schema_is_named_by_its_instantiation() {
+    use schematic::Schematic as _;
+
+    use crate::{conversation::label::LabelConfig, providers::mcp::McpProviderConfig};
+
+    assert_eq!(
+        MergeableMap::<LabelConfig>::schema_name().as_deref(),
+        Some("MergeableMap_LabelConfig")
+    );
+    assert_eq!(
+        MergeableMap::<McpProviderConfig>::schema_name().as_deref(),
+        Some("MergeableMap_McpProviderConfig")
+    );
+}
+
+/// An argument with no name of its own leaves the base name alone.
+#[test]
+fn a_generic_over_a_primitive_keeps_its_base_name() {
+    use schematic::Schematic as _;
+
+    assert_eq!(
+        MergeableMap::<String>::schema_name().as_deref(),
+        Some("MergeableMap")
+    );
+}
+
 #[test]
 fn deserialize_plain_map() {
     let v: MergeableMap<serde_json::Value> =
diff --git a/crates/jp_config/src/util.rs b/crates/jp_config/src/util.rs
index f4f5cef43..4897d5373 100644
--- a/crates/jp_config/src/util.rs
+++ b/crates/jp_config/src/util.rs
@@ -9,8 +9,7 @@ use std::{
 
 use camino::Utf8Path;
 use glob::glob;
-use indexmap::IndexMap;
-use schematic::{ConfigLoader, MergeError, MergeResult, PartialConfig};
+use schematic::{ConfigLoader, PartialConfig as _};
 use tracing::{debug, error, info, trace, warn};
 
 use crate::{
@@ -417,7 +416,7 @@ pub fn log_load_diagnostics(partial: &PartialAppConfig) {
         "Configuration details."
     );
 
-    for (name, tool) in &partial.conversation.tools.tools {
+    for (name, tool) in partial.conversation.tools.tools.iter() {
         if tool.source.is_none() {
             error!(
                 tool = %name,
@@ -615,36 +614,6 @@ fn dedup_keep_last(entries: Vec<ExtendsEntry>) -> Vec<ExtendsEntry> {
         .collect()
 }
 
-/// Merge [`IndexMap`]s of nested [`PartialConfig`]s.
-///
-/// # Errors
-///
-/// Returns an error if merging the partials fails, which returns a
-/// [`schematic::MergeError`].
-pub fn merge_nested_indexmap<V, C>(
-    prev: IndexMap<String, V>,
-    mut next: IndexMap<String, V>,
-    c: &C,
-) -> MergeResult<IndexMap<String, V>>
-where
-    V: PartialConfig<Context = C>,
-    C: Default,
-{
-    let mut prev = prev
-        .into_iter()
-        .map(|(name, mut prev)| {
-            if let Some(next) = next.shift_remove(&name) {
-                prev.merge(c, next).map_err(MergeError::new)?;
-            }
-
-            Ok((name, prev))
-        })
-        .collect::<Result<IndexMap<_, _>, _>>()?;
-
-    prev.append(&mut next);
-    Ok(Some(prev))
-}
-
 /// Define the name to serialize and deserialize for a unit variant.
 #[macro_export]
 macro_rules! named_unit_variant {
diff --git a/crates/jp_conversation/src/compat.rs b/crates/jp_conversation/src/compat.rs
index d5e4f534c..c74a47cc4 100644
--- a/crates/jp_conversation/src/compat.rs
+++ b/crates/jp_conversation/src/compat.rs
@@ -325,9 +325,59 @@ fn sole_matching_variant<'a>(union_type: &'a UnionType, value: &Value) -> Option
     let variants = || union_type.variants_types.iter().map(Box::as_ref);
 
     sole(variants().filter(|variant| !variant.is_null()))
+        .or_else(|| strategy_carrying_variant(union_type, value))
         .or_else(|| sole(variants().filter(|variant| accepts(&variant.ty, value))))
 }
 
+/// The variant of a collection that can state its own merge strategy.
+///
+/// A `MergeableMap` is the plain map beside a wrapper struct holding it under
+/// `value` next to the strategy.
+/// Both are objects on the wire, so shape alone leaves the union ambiguous, and
+/// every key inside a tool, server, alias or plugin would go unwalked: a stale
+/// one would then survive to fail typed deserialization, which discards the
+/// whole stored config rather than the key.
+///
+/// Told apart the way the wrapper's own deserializer does it: an object
+/// carrying both `value` and `strategy` is the wrapper, anything else is the
+/// map.
+/// An entry named `value` needs the sibling `strategy` before it reads as the
+/// wrapper, which is what keeps a tool called `value` addressable.
+///
+/// The pair is recognised by one side being a map rather than by the wrapper's
+/// own fields: the wrapper type is described once and referred to by name
+/// wherever it appears again, so most of its uses are a reference with no
+/// fields to inspect.
+fn strategy_carrying_variant<'a>(union_type: &'a UnionType, value: &Value) -> Option<&'a Schema> {
+    let variants = || {
+        union_type
+            .variants_types
+            .iter()
+            .map(Box::as_ref)
+            .filter(|variant| !variant.is_null())
+    };
+
+    let is_map = |schema: &Schema| matches!(schema.ty, SchemaType::Object(_));
+
+    let collection = sole(variants().filter(|variant| is_map(variant)))?;
+    let wrapper = sole(variants().filter(|variant| !is_map(variant)))?;
+
+    let stated = value.as_object().is_some_and(states_a_strategy);
+
+    Some(if stated { wrapper } else { collection })
+}
+
+/// Whether an object is a collection that states its own merge strategy, rather
+/// than the collection itself.
+///
+/// Both reach disk as a table, so the keys decide: the wrapper carries `value`
+/// beside `strategy`, which is how its own deserializer tells them apart.
+/// An entry named `value` needs the sibling `strategy` before it reads as the
+/// wrapper, so a tool called `value` stays addressable.
+fn states_a_strategy(obj: &serde_json::Map<String, Value>) -> bool {
+    obj.contains_key("value") && obj.contains_key("strategy")
+}
+
 /// The only item an iterator yields, if it yields exactly one.
 fn sole<'a>(mut variants: impl Iterator<Item = &'a Schema>) -> Option<&'a Schema> {
     match (variants.next(), variants.next()) {
@@ -392,7 +442,8 @@ fn strip_struct<'a>(
         return 0;
     };
 
-    let entry_schema = flattened_entry_schema(struct_type);
+    let flattened = flattened_field_schema(struct_type);
+    let entry_schema = flattened.and_then(map_value_schema);
     let has_flatten = struct_type.fields.values().any(|f| f.flatten);
 
     let mut stripped = if has_flatten {
@@ -403,6 +454,22 @@ fn strip_struct<'a>(
         before - obj.len()
     };
 
+    // A flattened map stating a strategy puts the wrapper's own keys where
+    // entries otherwise sit: `value` holds the map, and the metadata beside it
+    // says how it merges rather than naming an entry. Walking those keys as
+    // entries would take the map for a single one and delete every key in it.
+    if has_flatten && states_a_strategy(obj) {
+        if let Some(entry_schema) = entry_schema
+            && let Some(Value::Object(entries)) = obj.get_mut("value")
+        {
+            for entry in entries.values_mut() {
+                stripped += strip_schema(entry, entry_schema, enclosing);
+            }
+        }
+
+        return stripped;
+    }
+
     for (key, child) in obj.iter_mut() {
         // The flattened field's own name is not a key in the serialized form,
         // so a key matching it is an entry of the map it flattens, not that
@@ -426,7 +493,7 @@ fn strip_struct<'a>(
 /// flattens something other than a map — in each of those cases the shape of a
 /// leftover key is not knowable, and walking it against the wrong schema would
 /// delete valid data.
-fn flattened_entry_schema(struct_type: &StructType) -> Option<&Schema> {
+fn flattened_field_schema(struct_type: &StructType) -> Option<&Schema> {
     let mut flattened = struct_type
         .fields
         .values()
@@ -434,11 +501,33 @@ fn flattened_entry_schema(struct_type: &StructType) -> Option<&Schema> {
         .map(Box::as_ref);
 
     match (flattened.next(), flattened.next()) {
-        (Some(SchemaField { schema, .. }), None) => match &schema.ty {
+        (Some(SchemaField { schema, .. }), None) => Some(schema),
+        _ => None,
+    }
+}
+
+/// The schema of a map's values, for a map written either plainly or with a
+/// stated merge strategy.
+///
+/// A map that can state one is a union of the plain map and the wrapper holding
+/// it under `value`.
+/// Flattened, its entries are sibling keys of the struct around it, which is
+/// the plain map's shape, so that is the variant their values are walked
+/// against.
+fn map_value_schema(schema: &Schema) -> Option<&Schema> {
+    fn value_type(ty: &SchemaType) -> Option<&Schema> {
+        match ty {
             SchemaType::Object(object_type) => Some(&object_type.value_type),
             _ => None,
-        },
-        _ => None,
+        }
+    }
+
+    match &schema.ty {
+        SchemaType::Union(union_type) => union_type
+            .variants_types
+            .iter()
+            .find_map(|variant| value_type(&variant.ty)),
+        ty => value_type(ty),
     }
 }
 
diff --git a/crates/jp_conversation/src/compat_tests.rs b/crates/jp_conversation/src/compat_tests.rs
index a952fb559..0eb191614 100644
--- a/crates/jp_conversation/src/compat_tests.rs
+++ b/crates/jp_conversation/src/compat_tests.rs
@@ -244,6 +244,41 @@ fn strip_descends_into_a_tool_named_after_the_flattened_field() {
     );
 }
 
+#[test]
+fn strip_descends_into_a_flattened_map_stating_a_strategy() {
+    // Removing one of a conversation's tools records the map the user is left
+    // with, stamped `replace`. Flattened, that wrapper's own keys sit where
+    // tool names otherwise do, so `value` holds the map rather than a tool.
+    let schema = AppConfig::schema();
+    let mut value = json!({
+        "conversation": {
+            "tools": {
+                "value": {
+                    "bash": { "source": "local", "from_a_newer_jp": 1 }
+                },
+                "strategy": "replace"
+            }
+        }
+    });
+
+    let stripped = strip_unknown_fields(&mut value, &schema);
+    assert_eq!(stripped, 1);
+    assert_eq!(
+        value,
+        json!({
+            "conversation": {
+                "tools": {
+                    "value": {
+                        "bash": { "source": "local" }
+                    },
+                    "strategy": "replace"
+                }
+            }
+        }),
+        "the retained tool survives and the strategy is left alone"
+    );
+}
+
 #[test]
 fn strip_descends_into_array_items() {
     let schema = AppConfig::schema();
@@ -862,6 +897,32 @@ fn legacy_enable_strings_survive_compat_deserialization() {
     assert_eq!(tools["off_tool"].enable, Some(PartialEnableConfig::OFF));
 }
 
+#[test]
+fn a_removed_tool_leaves_the_others_standing() {
+    // Removing one of two tools stores the map the user is left with, stamped
+    // `replace`. Reading that back has to keep the tool they kept: an empty
+    // replacement would take every tool the conversation had.
+    let value = json!({
+        "conversation": {
+            "tools": {
+                "value": {
+                    "bash": { "source": "local", "from_a_newer_jp": 1 }
+                },
+                "strategy": "replace"
+            }
+        }
+    });
+
+    let config = deserialize_partial_config(value);
+    let tools = &config.conversation.tools.tools;
+
+    assert!(
+        tools.contains_key("bash"),
+        "the retained tool survives the read: {tools:?}"
+    );
+    assert_eq!(tools.len(), 1, "and nothing else joins it");
+}
+
 #[test]
 fn legacy_rule_bounds_survive_compat_deserialization() {
     use jp_config::conversation::compaction::RuleBound;
diff --git a/crates/jp_llm/src/tool/json_schema.rs b/crates/jp_llm/src/tool/json_schema.rs
index fda533054..042210dff 100644
--- a/crates/jp_llm/src/tool/json_schema.rs
+++ b/crates/jp_llm/src/tool/json_schema.rs
@@ -745,7 +745,7 @@ fn apply_config_fields(
             .cloned()
             .unwrap_or_default();
 
-        for (name, property) in &config.properties {
+        for (name, property) in config.properties.iter() {
             let path = format!("{path}.properties.{name}");
             let merged = match properties.get(name) {
                 Some(source) => node_with_override(&path, source, root, property)?,