fix: address PR review — legacy teardown, generic agent, ~/.specify paths, 3-segment commands_dir, full file tracking

- Legacy --ai teardown: detect empty tracked files and fall back to
  AGENT_CONFIG-based directory removal during agent switch
- --agent generic: falls through to legacy flow (no embedded pack)
- User/catalog dirs: use ~/.specify/ instead of platformdirs for
  consistency with extensions/presets
- DefaultBootstrap: join all path segments after first for COMMANDS_SUBDIR
  (fixes 3+-segment commands_dir like .tabnine/agent/commands)
- agent_add --from: validate manifest.id matches provided agent_id
- finalize_setup: track all files from setup(), not just agent-root files
- setup() docstring: reference --agent not --ai
- AGENTS.md: document generic agent fallback behavior

AGENTS.md

@@ -440,7 +440,7 @@ specify init my-project --agent claude          # Pack-based flow (with file tra
 specify init --here --agent gemini --ai-skills  # With skills
 ```
 
-`--agent` and `--ai` are mutually exclusive. When `--agent` is used, `init-options.json` gains `"agent_pack": true`.
+`--agent` and `--ai` are mutually exclusive. When `--agent` is used, `init-options.json` gains `"agent_pack": true`. The `generic` agent (which requires `--ai-commands-dir`) falls through to the legacy flow since it has no embedded pack.
 
 ### `specify agent` subcommands