feat(start-work): add auto_commit config option

Add start_work.auto_commit configuration option to allow users to
disable the automatic commit step in the /start-work workflow.

When auto_commit is false:
- STEP 8: COMMIT ATOMIC UNIT is removed from orchestrator reminder
- STEP 9: PROCEED TO NEXT TASK becomes STEP 8

Resolves #2197

src/hooks/atlas/atlas-hook.ts

@@ -7,6 +7,7 @@ import type { AtlasHookOptions, SessionState } from "./types"
 export function createAtlasHook(ctx: PluginInput, options?: AtlasHookOptions) {
   const sessions = new Map<string, SessionState>()
   const pendingFilePaths = new Map<string, string>()
+  const autoCommit = options?.autoCommit ?? true
 
   function getState(sessionID: string): SessionState {
     let state = sessions.get(sessionID)
@@ -20,6 +21,6 @@ export function createAtlasHook(ctx: PluginInput, options?: AtlasHookOptions) {
   return {
     handler: createAtlasEventHandler({ ctx, options, sessions, getState }),
     "tool.execute.before": createToolExecuteBeforeHandler({ ctx, pendingFilePaths }),
-    "tool.execute.after": createToolExecuteAfterHandler({ ctx, pendingFilePaths }),
+    "tool.execute.after": createToolExecuteAfterHandler({ ctx, pendingFilePaths, autoCommit }),
   }
 }