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/tools/index.d.ts

@@ -7,6 +7,7 @@ import './agent';
 import './memory';
 import './skills';
 import './prd';
+import './search';
 export { ALL_TOOLS, executeTool, ToolDefinition } from './registry';
 export { ToolContext, MemoryUpdate } from './context';
 export { PROTECTED_GITEA_REPOS, PROTECTED_COOLIFY_PROJECT, PROTECTED_COOLIFY_APPS, assertGiteaWritable, assertCoolifyDeployable } from './security';