docs: correct the module lists in AGENTS.md and CLAUDE.md

CLAUDE.md

@@ -13,10 +13,11 @@ and the Gitea token scope. Auth modes: admin-token (`GITEA_TOKEN` / static
 `MCP_BEARER_TOKEN`) and per-user OAuth on HTTP (user's own Gitea token).
 
 The project is mid-rebuild (chunk plan in `docs/audit.md`). Built so far: tooling,
-`config.py`, `identity.py`, `errors.py`, `catalog/model.py`, `cli.py` skeleton,
-audit/security/limits helpers. Planned: catalog generator (B2), executor (B3),
-server and transports (B4), OAuth (B5), setup command (B6), integration harness
-and suite (B7, B8), smoke tests (B9), CI (B10), docs (B11).
+`config.py`, `identity.py`, `errors.py`, the generated catalog (`catalog/`), the
+Gitea executor (`gitea/`), the setup command (`setup_cmd.py`, `setup_snippets.py`,
+`setup_template.py`), the integration harness, CI and audit/security/limits
+helpers. Planned: server and transports (B4), OAuth (B5), smoke tests (B9),
+docs (B11).
 
 ## Commands
 
@@ -27,20 +28,27 @@ make format             # ruff format + ruff check --fix
 make test               # uv run pytest (coverage gate)
 make test-integration   # AEGIS_INTEGRATION=1, needs Docker
 make run                # uv run aegis-gitea-mcp serve (not implemented until B4)
+uv run python scripts/generate_catalog.py --check   # catalog matches the spec
 make validate-audit     # verify audit hash chain
 uv run pytest tests/test_config.py::test_defaults -v   # single test
 ```
 
-## Architecture (target)
+## Architecture
 
-- `catalog/`: `Operation`/`Parameter` model (done), generated `tools.json` and
-  loader (B2).
-- `gitea/` executor: path templating, query/JSON/multipart, Sudo header,
-  pagination, error mapping, limits, masking, result envelope (B3).
-- Server: low-level SDK `Server` with one `on_list_tools` and one `on_call_tool`
-  dispatcher, jsonschema validation, audit, `is_error` results for tool
-  failures, `gitea_api_request` escape-hatch tool (B4).
-- Auth: static bearer verifier and OAuth provider with encrypted token store (B5).
+- `catalog/` (done): `model.py` (`Operation`, `Parameter`), `build.py` (swagger to
+  catalog, MCP annotations), `naming.py`, `schema.py`, generated `tools.json`
+  (regenerate with `uv run python scripts/generate_catalog.py`, check with
+  `--check`) and the loader in `__init__.py`.
+- `gitea/` (done): `executor.py` (HTTP call, result envelope, redaction, size
+  limits, `CREDENTIAL_ISSUING_OPERATIONS`), `encoding.py` (path, query, body and
+  upload building, `SLASH_ROUTES`), `pagination.py`, `redaction.py`.
+- `setup_cmd.py`, `setup_snippets.py`, `setup_template.py` (done): the `setup`
+  command, its client snippets and the built-in `.env` template.
+- Server (B4, planned): low-level SDK `Server` with one `on_list_tools` and one
+  `on_call_tool` dispatcher, jsonschema validation, audit, `is_error` results for
+  tool failures, `gitea_api_request` escape-hatch tool.
+- Auth (B5, planned): static bearer verifier and OAuth provider with encrypted
+  token store.
 - Core helpers (done): `config.py` (`Settings`, `get_settings()`,
   `reset_settings()`), `identity.py`, `errors.py` (`ToolError`,
   `GiteaAPIError`), `audit.py`, `security.py`, `response_limits.py`,