feat(config, mcp)!: Implement nested inheritance for MCP config

Cargo.toml

@@ -63,6 +63,7 @@ openai = { git = "https://github.com/JeanMertz/openai", branch = "tmp", default-
 openai_responses = { git = "https://github.com/JeanMertz/openai-responses-rs", default-features = false } # <https://github.com/m1guelpf/openai-responses-rs/pull/6>
 path-clean = { version = "1", default-features = false }
 percent-encoding = { version = "2", default-features = false }
+pretty_assertions = { version = "1", default-features = false }
 quick-xml = { version = "0.38", default-features = false }
 reqwest = { version = "0.12", default-features = false }
 reqwest-eventsource = { version = "0.6", default-features = false }
@@ -87,7 +88,6 @@ timeago = { version = "0.5", default-features = false }
 tokio = { version = "1", default-features = false, features = ["full"] }
 tokio-util = { version = "0.7", default-features = false }
 toml = { version = "0.9", default-features = false }
-toml_edit = { version = "0.23", default-features = false }
 tracing = { version = "0.1", default-features = false }
 tracing-subscriber = { version = "0.3", default-features = false }
 typetag = { version = "0.2", default-features = false }

crates/jp_cli/Cargo.toml

@@ -67,7 +67,7 @@ thiserror = { workspace = true }
 time = { workspace = true, features = ["local-offset"] }
 timeago = { workspace = true }
 tokio = { workspace = true }
-toml = { workspace = true }
+toml = { workspace = true, features = ["preserve_order"] }
 tracing = { workspace = true }
 tracing-subscriber = { workspace = true, features = [
     "ansi",

crates/jp_cli/src/cmd/query.rs

@@ -16,7 +16,12 @@ use futures::StreamExt as _;
 use jp_config::{
     assignment::{AssignKeyValue as _, KvAssignment},
     assistant::Instructions,
-    expand_tilde, PartialConfig,
+    expand_tilde,
+    mcp::{
+        server::{Server, ToolId},
+        ServerId,
+    },
+    PartialConfig,
 };
 use jp_conversation::{
     thread::{Thread, ThreadBuilder},
@@ -834,12 +839,24 @@ async fn list_enabled_tools(ctx: &Ctx) -> Result<Vec<Tool>> {
     for tool in all_tools {
         let tool_id = McpToolId::new(&*tool.name);
         let server_id = ctx.mcp_client.get_tool_server_id(&tool_id).await?;
-        let server_cfg = ctx.config.mcp.get_server_with_defaults(server_id.as_str());
+        let server_defaults = Server::default();
+        let server_cfg = ctx
+            .config
+            .mcp
+            .servers
+            .get(&ServerId::new(server_id.as_str()))
+            .unwrap_or(&server_defaults);
+
         if !server_cfg.enable {
             continue;
         }
 
-        let tool_cfg = server_cfg.get_tool_with_defaults(&tool.name);
+        let tool_defaults = jp_config::mcp::server::tool::Tool::default();
+        let tool_cfg = server_cfg
+            .tools
+            .get(&ToolId::new(tool.name.as_ref()))
+            .unwrap_or(&tool_defaults);
+
         if !tool_cfg.enable {
             continue;
         }

crates/jp_cli/src/cmd/query/event.rs

@@ -9,8 +9,12 @@ use hex::ToHex as _;
 use inquire::Confirm;
 use jp_config::{
     mcp::{
-        server::{checksum::Algorithm, tool},
-        tool_call,
+        server::{
+            checksum::Algorithm,
+            tool::{self, Tool},
+            Server, ToolId,
+        },
+        tool_call, ServerId,
     },
     style::LinkStyle,
 };
@@ -110,8 +114,19 @@ async fn build_tool_call_result(
 ) -> Result<Option<String>, Error> {
     let tool_id = McpToolId::new(&call.name);
     let server_id = ctx.mcp_client.get_tool_server_id(&tool_id).await?;
-    let server_cfg = ctx.config.mcp.get_server_with_defaults(server_id.as_str());
-    let tool_cfg = server_cfg.get_tool_with_defaults(&call.name);
+    let server_defaults = Server::default();
+    let server_cfg = ctx
+        .config
+        .mcp
+        .servers
+        .get(&ServerId::new(server_id.as_str()))
+        .unwrap_or(&server_defaults);
+
+    let tool_defaults = Tool::default();
+    let tool_cfg = server_cfg
+        .tools
+        .get(&ToolId::new(&call.name))
+        .unwrap_or(&tool_defaults);
 
     let mut lines = result.content.trim().lines().collect::<Vec<_>>();
     let ext = lines
@@ -203,8 +218,19 @@ async fn call_tool(ctx: &Ctx, mut call: ToolCallRequest) -> Result<ToolCallResul
     info!(tool = %call.name, arguments = %call.arguments, "Calling tool.");
     let tool_id = McpToolId::new(&call.name);
     let server_id = ctx.mcp_client.get_tool_server_id(&tool_id).await?;
-    let server_cfg = ctx.config.mcp.get_server_with_defaults(server_id.as_str());
-    let mut tool_cfg = server_cfg.get_tool_with_defaults(&call.name);
+    let server_defaults = Server::default();
+    let server_cfg = ctx
+        .config
+        .mcp
+        .servers
+        .get(&ServerId::new(server_id.as_str()))
+        .unwrap_or(&server_defaults);
+
+    let mut tool_cfg = server_cfg
+        .tools
+        .get(&ToolId::new(&call.name))
+        .cloned()
+        .unwrap_or_default();
 
     if let Some(checksum) = &server_cfg.binary_checksum {
         let path = get_tool_binary_path(ctx, &tool_id).await?;

crates/jp_config/Cargo.toml

@@ -26,13 +26,14 @@ serde = { workspace = true, features = ["std"] }
 serde_json = { workspace = true }
 serde_yaml = { workspace = true }
 thiserror = { workspace = true }
-toml = { workspace = true, features = ["parse", "serde", "display"] }
-toml_edit = { workspace = true, features = ["serde", "parse", "display"] }
+toml = { workspace = true, features = ["parse", "serde", "display", "preserve_order"] }
 tracing = { workspace = true }
 url = { workspace = true, features = ["serde"] }
 
 [dev-dependencies]
-insta = { workspace = true }
+indoc = { workspace = true }
+insta = { workspace = true, features = ["json", "toml", "colors"] }
+pretty_assertions = { workspace = true, features = ["std"] }
 serial_test = { workspace = true }
 tempfile = { workspace = true }
 test-log = { workspace = true }

crates/jp_config/src/fs.rs

@@ -99,7 +99,7 @@ impl ConfigFile {
         f(&mut value)?;
 
         self.content = match self.format {
-            Format::Toml => toml_edit::ser::to_string_pretty(&value)?,
+            Format::Toml => toml::ser::to_string_pretty(&value)?,
             Format::Json => serde_json::to_string_pretty(&value)?,
             Format::Json5 => json5::to_string(&value)?,
             Format::Yaml => serde_yaml::to_string(&value)?,

crates/jp_config/src/map.rs

@@ -158,6 +158,34 @@ where
     }
 }
 
+impl<K, V> FromIterator<(K, V)> for ConfigMapPartial<K, V>
+where
+    K: Hash + Eq,
+    V: Partial,
+{
+    /// Create a `ConfigMapPartial` from the sequence of key-value pairs in the
+    /// iterable.
+    ///
+    /// `from_iter` uses the same logic as `extend`. See
+    /// [`extend`][IndexMap::extend] for more details.
+    fn from_iter<I: IntoIterator<Item = (K, V)>>(iterable: I) -> Self {
+        let iter = iterable.into_iter();
+        let (low, _) = iter.size_hint();
+        let mut map = IndexMap::with_capacity_and_hasher(low, <_>::default());
+        map.extend(iter);
+        Self(map)
+    }
+}
+
+impl<K, V: Partial> IntoIterator for ConfigMapPartial<K, V> {
+    type Item = (K, V);
+    type IntoIter = indexmap::map::IntoIter<K, V>;
+
+    fn into_iter(self) -> Self::IntoIter {
+        self.0.into_iter()
+    }
+}
+
 // See: <https://serde.rs/deserialize-map.html>
 struct ConfigMapVisitor<K, V: Config> {
     marker: PhantomData<fn() -> ConfigMap<K, V>>,