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/cli/run/completion.test.ts

@@ -30,20 +30,20 @@ const createMockContext = (overrides: {
 
 describe("checkCompletionConditions", () => {
   it("returns true when no todos and no children", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext()
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(true)
   })
 
   it("returns false when incomplete todos exist", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext({
       todo: [
@@ -53,15 +53,15 @@ describe("checkCompletionConditions", () => {
     })
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(false)
   })
 
   it("returns true when all todos completed or cancelled", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext({
       todo: [
@@ -71,15 +71,15 @@ describe("checkCompletionConditions", () => {
     })
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(true)
   })
 
   it("returns false when child session is busy", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext({
       childrenBySession: {
@@ -90,15 +90,15 @@ describe("checkCompletionConditions", () => {
     })
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(false)
   })
 
   it("returns true when all children idle", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext({
       childrenBySession: {
@@ -113,15 +113,15 @@ describe("checkCompletionConditions", () => {
     })
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(true)
   })
 
   it("returns false when grandchild is busy (recursive)", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext({
       childrenBySession: {
@@ -136,15 +136,15 @@ describe("checkCompletionConditions", () => {
     })
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(false)
   })
 
   it("returns true when all descendants idle (recursive)", async () => {
-    // #given
+    // given
     spyOn(console, "log").mockImplementation(() => {})
     const ctx = createMockContext({
       childrenBySession: {
@@ -161,10 +161,10 @@ describe("checkCompletionConditions", () => {
     })
     const { checkCompletionConditions } = await import("./completion")
 
-    // #when
+    // when
     const result = await checkCompletionConditions(ctx)
 
-    // #then
+    // then
     expect(result).toBe(true)
   })
 })