wire up /agent/execute and /agent/stop endpoints

- Add runSessionAgent: streaming variant of runAgent that PATCHes VIBN DB
  after every LLM turn and tool call so frontend can poll live output
- Track changed files from write_file / replace_in_file tool calls
- Add /agent/execute: receives sessionId + giteaRepo + task, clones repo,
  scopes workspace to appPath, runs Coder agent async (returns 202 immediately)
- Add /agent/stop: sets stopped flag; agent checks between turns and exits cleanly
- Agent does NOT commit on completion — leaves changes for user review/approval

Made-with: Cursor

dist/atlas.d.ts

@@ -18,4 +18,6 @@ export interface AtlasChatResult {
 }
 export declare function atlasChat(sessionId: string, userMessage: string, ctx: ToolContext, opts?: {
     preloadedHistory?: LLMMessage[];
+    /** When true, the user message is an internal init trigger and should not be stored in history */
+    isInit?: boolean;
 }): Promise<AtlasChatResult>;