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

AGENTS.md

@@ -47,26 +47,33 @@ the FastAPI adapter and the "core stays web-free" boundary.
 
 ```
 src/aegis_gitea_mcp/
-  catalog/      generated tool catalog: model.py (done), tools.json + loader (chunk B2)
+  catalog/        generated tool catalog: model.py (Operation, Parameter), build.py
-  gitea/        executor: templating, HTTP, pagination, errors, envelope (chunk B3)
+                  (swagger to catalog, annotations), naming.py, schema.py,
-  server.py     SDK low-level Server, list/call dispatch, filters (chunk B4)
+                  tools.json (generated, never hand-edited), __init__.py (loader)
-  transports    stdio entry, streamable HTTP app, /health, bind checks (chunk B4)
+  gitea/          executor: executor.py (HTTP, envelope, redaction, limits),
-  oauth/        SDK OAuth provider proxying Gitea, token store, verifier (chunk B5)
+                  encoding.py (path, query, body, upload building), pagination.py,
-  setup.py      `aegis-gitea-mcp setup` command (chunk B6)
+                  redaction.py (exact-match secret redaction)
-  cli.py        argparse entry: serve (default), setup, version (skeleton done)
+  setup_cmd.py    `aegis-gitea-mcp setup`: verify instance, register OAuth app, write .env
-  config.py     pydantic-settings Settings, get_settings()/reset_settings()
+  setup_snippets.py  client config snippets printed by setup
-  identity.py   Identity(login, mode, token) carried through each call
+  setup_template.py  built-in .env template used by setup
-  errors.py     ToolError, GiteaAPIError(status, kind, message)
+  cli.py          argparse entry: serve (default), setup, version
-  audit.py      hash-chained audit log; security.py secret masking;
+  config.py       pydantic-settings Settings, get_settings()/reset_settings()
+  identity.py     Identity(login, mode, token) carried through each call
+  errors.py       ToolError, GiteaAPIError(status, kind, message)
+  audit.py        hash-chained audit log; security.py secret masking;
   response_limits.py, rate_limit.py (HTTP), request_context.py, logging_utils.py
-scripts/        generate_catalog.py (B2), validate_audit_log.py, check_docs.py (B11)
+  server.py, transports, oauth/   planned (chunks B4, B5), not present yet
+scripts/        generate_catalog.py, validate_audit_log.py, ci/, check_docs.py (B11)
 spec/           pinned Gitea swagger
+tests/integration/  live Gitea in Docker (harness.py), opt-in
 ```
 
-Modules marked with a chunk id do not exist yet. Request flow (target):
+Modules marked planned do not exist yet. Request flow (target):
 client -> SDK transport and auth verifier -> `Identity` -> toolset/read-only
 filters -> schema validation -> executor (Gitea call with the identity's token,
 optional `sudo`) -> limits and masking -> result envelope (ADR 0005) -> audit.
+The executor and the catalog exist; the server and transports that connect them
+to MCP clients do not yet.
 
 ## Commands
 

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,
+`config.py`, `identity.py`, `errors.py`, the generated catalog (`catalog/`), the
-audit/security/limits helpers. Planned: catalog generator (B2), executor (B3),
+Gitea executor (`gitea/`), the setup command (`setup_cmd.py`, `setup_snippets.py`,
-server and transports (B4), OAuth (B5), setup command (B6), integration harness
+`setup_template.py`), the integration harness, CI and audit/security/limits
-and suite (B7, B8), smoke tests (B9), CI (B10), docs (B11).
+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
+- `catalog/` (done): `model.py` (`Operation`, `Parameter`), `build.py` (swagger to
-  loader (B2).
+  catalog, MCP annotations), `naming.py`, `schema.py`, generated `tools.json`
-- `gitea/` executor: path templating, query/JSON/multipart, Sudo header,
+  (regenerate with `uv run python scripts/generate_catalog.py`, check with
-  pagination, error mapping, limits, masking, result envelope (B3).
+  `--check`) and the loader in `__init__.py`.
-- Server: low-level SDK `Server` with one `on_list_tools` and one `on_call_tool`
+- `gitea/` (done): `executor.py` (HTTP call, result envelope, redaction, size
-  dispatcher, jsonschema validation, audit, `is_error` results for tool
+  limits, `CREDENTIAL_ISSUING_OPERATIONS`), `encoding.py` (path, query, body and
-  failures, `gitea_api_request` escape-hatch tool (B4).
+  upload building, `SLASH_ROUTES`), `pagination.py`, `redaction.py`.
-- Auth: static bearer verifier and OAuth provider with encrypted token store (B5).
+- `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`,