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/doctor/checks/mcp-oauth.test.ts

@@ -4,11 +4,11 @@ import * as mcpOauth from "./mcp-oauth"
 describe("mcp-oauth check", () => {
   describe("getMcpOAuthCheckDefinition", () => {
     it("returns check definition with correct properties", () => {
-      // #given
-      // #when getting definition
+      // given
+      // when getting definition
       const def = mcpOauth.getMcpOAuthCheckDefinition()
 
-      // #then should have correct structure
+      // then should have correct structure
       expect(def.id).toBe("mcp-oauth-tokens")
       expect(def.name).toBe("MCP OAuth Tokens")
       expect(def.category).toBe("tools")
@@ -25,19 +25,19 @@ describe("mcp-oauth check", () => {
     })
 
     it("returns skip when no tokens stored", async () => {
-      // #given no OAuth tokens configured
+      // given no OAuth tokens configured
       readStoreSpy = spyOn(mcpOauth, "readTokenStore").mockReturnValue(null)
 
-      // #when checking OAuth tokens
+      // when checking OAuth tokens
       const result = await mcpOauth.checkMcpOAuthTokens()
 
-      // #then should skip
+      // then should skip
       expect(result.status).toBe("skip")
       expect(result.message).toContain("No OAuth")
     })
 
     it("returns pass when all tokens valid", async () => {
-      // #given valid tokens with future expiry (expiresAt is in epoch seconds)
+      // given valid tokens with future expiry (expiresAt is in epoch seconds)
       const futureTime = Math.floor(Date.now() / 1000) + 3600
       readStoreSpy = spyOn(mcpOauth, "readTokenStore").mockReturnValue({
         "example.com/resource1": {
@@ -50,17 +50,17 @@ describe("mcp-oauth check", () => {
         },
       })
 
-      // #when checking OAuth tokens
+      // when checking OAuth tokens
       const result = await mcpOauth.checkMcpOAuthTokens()
 
-      // #then should pass
+      // then should pass
       expect(result.status).toBe("pass")
       expect(result.message).toContain("2")
       expect(result.message).toContain("valid")
     })
 
     it("returns warn when some tokens expired", async () => {
-      // #given mix of valid and expired tokens (expiresAt is in epoch seconds)
+      // given mix of valid and expired tokens (expiresAt is in epoch seconds)
       const futureTime = Math.floor(Date.now() / 1000) + 3600
       const pastTime = Math.floor(Date.now() / 1000) - 3600
       readStoreSpy = spyOn(mcpOauth, "readTokenStore").mockReturnValue({
@@ -74,10 +74,10 @@ describe("mcp-oauth check", () => {
         },
       })
 
-      // #when checking OAuth tokens
+      // when checking OAuth tokens
       const result = await mcpOauth.checkMcpOAuthTokens()
 
-      // #then should warn
+      // then should warn
       expect(result.status).toBe("warn")
       expect(result.message).toContain("1")
       expect(result.message).toContain("expired")
@@ -87,23 +87,23 @@ describe("mcp-oauth check", () => {
     })
 
     it("returns pass when tokens have no expiry", async () => {
-      // #given tokens without expiry info
+      // given tokens without expiry info
       readStoreSpy = spyOn(mcpOauth, "readTokenStore").mockReturnValue({
         "example.com/resource1": {
           accessToken: "token1",
         },
       })
 
-      // #when checking OAuth tokens
+      // when checking OAuth tokens
       const result = await mcpOauth.checkMcpOAuthTokens()
 
-      // #then should pass (no expiry = assume valid)
+      // then should pass (no expiry = assume valid)
       expect(result.status).toBe("pass")
       expect(result.message).toContain("1")
     })
 
     it("includes token details in output", async () => {
-      // #given multiple tokens
+      // given multiple tokens
       const futureTime = Math.floor(Date.now() / 1000) + 3600
       readStoreSpy = spyOn(mcpOauth, "readTokenStore").mockReturnValue({
         "api.example.com/v1": {
@@ -116,10 +116,10 @@ describe("mcp-oauth check", () => {
         },
       })
 
-      // #when checking OAuth tokens
+      // when checking OAuth tokens
       const result = await mcpOauth.checkMcpOAuthTokens()
 
-      // #then should list tokens in details
+      // then should list tokens in details
       expect(result.details).toBeDefined()
       expect(result.details?.length).toBeGreaterThan(0)
       expect(