refactor: major codebase cleanup - BDD comments, file splitting, bug fixes (#1350)

* style(tests): normalize BDD comments from '// #given' to '// given'

- Replace 4,668 Python-style BDD comments across 107 test files
- Patterns changed: // #given -> // given, // #when -> // when, // #then -> // then
- Also handles no-space variants: //#given -> // given

* fix(rules-injector): prefer output.metadata.filePath over output.title

- Extract file path resolution to dedicated output-path.ts module
- Prefer metadata.filePath which contains actual file path
- Fall back to output.title only when metadata unavailable
- Fixes issue where rules weren't injected when tool output title was a label

* feat(slashcommand): add optional user_message parameter

- Add user_message optional parameter for command arguments
- Model can now call: command='publish' user_message='patch'
- Improves error messages with clearer format guidance
- Helps LLMs understand correct parameter usage

* feat(hooks): restore compaction-context-injector hook

- Restore hook deleted in cbbc7bd0 for session compaction context
- Injects 7 mandatory sections: User Requests, Final Goal, Work Completed,
  Remaining Tasks, Active Working Context, MUST NOT Do, Agent Verification State
- Re-register in hooks/index.ts and main plugin entry

* refactor(background-agent): split manager.ts into focused modules

- Extract constants.ts for TTL values and internal types (52 lines)
- Extract state.ts for TaskStateManager class (204 lines)
- Extract spawner.ts for task creation logic (244 lines)
- Extract result-handler.ts for completion handling (265 lines)
- Reduce manager.ts from 1377 to 755 lines (45% reduction)
- Maintain backward compatible exports

* refactor(agents): split prometheus-prompt.ts into subdirectory

- Move 1196-line prometheus-prompt.ts to prometheus/ subdirectory
- Organize prompt sections into separate files for maintainability
- Update agents/index.ts exports

* refactor(delegate-task): split tools.ts into focused modules

- Extract categories.ts for category definitions and routing
- Extract executor.ts for task execution logic
- Extract helpers.ts for utility functions
- Extract prompt-builder.ts for prompt construction
- Reduce tools.ts complexity with cleaner separation of concerns

* refactor(builtin-skills): split skills.ts into individual skill files

- Move each skill to dedicated file in skills/ subdirectory
- Create barrel export for backward compatibility
- Improve maintainability with focused skill modules

* chore: update import paths and lockfile

- Update prometheus import path after refactor
- Update bun.lock

* fix(tests): complete BDD comment normalization

- Fix remaining #when/#then patterns missed by initial sed
- Affected: state.test.ts, events.test.ts

---------

Co-authored-by: justsisyphus <justsisyphus@users.noreply.github.com>

src/features/mcp-oauth/discovery.test.ts

@@ -13,7 +13,7 @@ describe("discoverOAuthServerMetadata", () => {
   })
 
   test("returns endpoints from PRM + AS discovery", () => {
-    // #given
+    // given
     const resource = "https://mcp.example.com"
     const prmUrl = new URL("/.well-known/oauth-protected-resource", resource).toString()
     const authServer = "https://auth.example.com"
@@ -39,9 +39,9 @@ describe("discoverOAuthServerMetadata", () => {
     }
     Object.defineProperty(globalThis, "fetch", { value: fetchMock, configurable: true })
 
-    // #when
+    // when
     return discoverOAuthServerMetadata(resource).then((result) => {
-      // #then
+      // then
       expect(result).toEqual({
         authorizationEndpoint: "https://auth.example.com/authorize",
         tokenEndpoint: "https://auth.example.com/token",
@@ -53,7 +53,7 @@ describe("discoverOAuthServerMetadata", () => {
   })
 
   test("falls back to RFC 8414 when PRM returns 404", () => {
-    // #given
+    // given
     const resource = "https://mcp.example.com"
     const prmUrl = new URL("/.well-known/oauth-protected-resource", resource).toString()
     const asUrl = new URL("/.well-known/oauth-authorization-server", resource).toString()
@@ -77,9 +77,9 @@ describe("discoverOAuthServerMetadata", () => {
     }
     Object.defineProperty(globalThis, "fetch", { value: fetchMock, configurable: true })
 
-    // #when
+    // when
     return discoverOAuthServerMetadata(resource).then((result) => {
-      // #then
+      // then
       expect(result).toEqual({
         authorizationEndpoint: "https://mcp.example.com/authorize",
         tokenEndpoint: "https://mcp.example.com/token",
@@ -91,7 +91,7 @@ describe("discoverOAuthServerMetadata", () => {
   })
 
   test("throws when both PRM and AS discovery return 404", () => {
-    // #given
+    // given
     const resource = "https://mcp.example.com"
     const prmUrl = new URL("/.well-known/oauth-protected-resource", resource).toString()
     const asUrl = new URL("/.well-known/oauth-authorization-server", resource).toString()
@@ -104,15 +104,15 @@ describe("discoverOAuthServerMetadata", () => {
     }
     Object.defineProperty(globalThis, "fetch", { value: fetchMock, configurable: true })
 
-    // #when
+    // when
     const result = discoverOAuthServerMetadata(resource)
 
-    // #then
+    // then
     return expect(result).rejects.toThrow("OAuth authorization server metadata not found")
   })
 
   test("throws when AS metadata is malformed", () => {
-    // #given
+    // given
     const resource = "https://mcp.example.com"
     const prmUrl = new URL("/.well-known/oauth-protected-resource", resource).toString()
     const authServer = "https://auth.example.com"
@@ -131,15 +131,15 @@ describe("discoverOAuthServerMetadata", () => {
     }
     Object.defineProperty(globalThis, "fetch", { value: fetchMock, configurable: true })
 
-    // #when
+    // when
     const result = discoverOAuthServerMetadata(resource)
 
-    // #then
+    // then
     return expect(result).rejects.toThrow("token_endpoint")
   })
 
   test("caches discovery results per resource URL", () => {
-    // #given
+    // given
     const resource = "https://mcp.example.com"
     const prmUrl = new URL("/.well-known/oauth-protected-resource", resource).toString()
     const authServer = "https://auth.example.com"
@@ -164,11 +164,11 @@ describe("discoverOAuthServerMetadata", () => {
     }
     Object.defineProperty(globalThis, "fetch", { value: fetchMock, configurable: true })
 
-    // #when
+    // when
     return discoverOAuthServerMetadata(resource)
       .then(() => discoverOAuthServerMetadata(resource))
       .then(() => {
-        // #then
+        // then
         expect(calls).toEqual([prmUrl, asUrl])
       })
   })