refactor: split tools.ts into registry-based domain files

Replaces the single 800-line tools.ts and its switch dispatcher with a
Theia-inspired registry pattern — each tool domain is its own file, and
dispatch is a plain Map.get() call with no central routing function.

New structure in src/tools/:
  registry.ts   — ToolDefinition (with handler), registerTool(), executeTool(), ALL_TOOLS
  context.ts    — ToolContext, MemoryUpdate interfaces
  security.ts   — PROTECTED_* constants + assertGiteaWritable/assertCoolifyDeployable
  utils.ts      — safeResolve(), EXCLUDED set
  file.ts       — read_file, write_file, replace_in_file, list_directory, find_files, search_code
  shell.ts      — execute_command
  git.ts        — git_commit_and_push
  coolify.ts    — coolify_*, list_all_apps, get_app_status, deploy_app
  gitea.ts      — gitea_*, list_repos, list_all_issues, read_repo_file
  agent.ts      — spawn_agent, get_job_status
  memory.ts     — save_memory
  index.ts      — barrel with side-effect imports + re-exports

Adding a new tool now requires only a new file + registerTool() call.
No switch statement, no shared array to edit. External API unchanged.

Made-with: Cursor

src/tools/index.ts

@@ -0,0 +1,14 @@
+// Import domain files first — side effects register each tool into the registry.
+// Order determines ALL_TOOLS array order (informational only).
+import './file';
+import './shell';
+import './git';
+import './gitea';
+import './coolify';
+import './agent';
+import './memory';
+
+// Re-export the public API — identical surface to the old tools.ts
+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';