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/agents/atlas.js

@@ -6,5 +6,5 @@ const registry_1 = require("./registry");
     description: 'PRD agent — guides users through structured product discovery and produces a comprehensive requirements document',
     model: 'A', // Gemini Flash — fast, conversational, cost-effective for dialogue
     promptId: 'atlas',
-    tools: (0, registry_1.pick)(['finalize_prd'])
+    tools: (0, registry_1.pick)(['web_search', 'finalize_prd'])
 });