feat(core): single-source data_dir/repos_dir via castle.yaml

The `castle` CLI and the `castle-api` service are two independent in-process
drivers of `castle_core`. Each resolved DATA_DIR/REPOS_DIR at import time from
its own process env (default /data/castle), persisted nowhere — so they silently
diverged, and `apply`/dashboard-apply crashed on a non-existent /data.

Make the loaded CastleConfig the single source of truth:
- Resolve data_dir/repos_dir only in load_config (env > castle.yaml > default),
  anchored to the config root; drop the DATA_DIR/REPOS_DIR module globals and the
  import-time file read entirely — no global twin that can disagree with the file.
- Thread config.data_dir/repos_dir through ensure_dirs, _env_context, tls_dir_for
  (now unified — deploy no longer inlines the tls path), and create/add/clone.
- ensure_dirs raises an actionable CastleDirError instead of a bare PermissionError;
  the api surfaces it as 422.
- doctor: "data dir writable" check + WARN when CASTLE_DATA_DIR/REPOS_DIR env
  overrides the file (the one remaining cross-process divergence vector).
- install.sh persists data_dir/repos_dir into castle.yaml (idempotent, non-default).
- Docs: registry.md globals + AGENTS.md roots.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

cli/src/castle_cli/commands/doctor.py

@@ -12,6 +12,7 @@ doubles as a scriptable smoke test after `./install.sh` or `castle apply`.
 from __future__ import annotations
 
 import argparse
+import os
 import shutil
 import socket
 from dataclasses import dataclass
@@ -136,6 +137,37 @@ def _check_configuration(config) -> list[Check]:
             )
         )
 
+    # data dir must exist and be writable — the exact condition that crashes apply
+    # (ensure_dirs) when data_dir points at a non-existent volume like /data.
+    ddir = config.data_dir
+    if ddir.is_dir() and os.access(ddir, os.W_OK):
+        checks.append(Check(OK, "data dir writable", detail=str(ddir)))
+    else:
+        checks.append(
+            Check(
+                FAIL,
+                "data dir missing or not writable",
+                detail=str(ddir),
+                hint=f"set data_dir: in ~/.castle/castle.yaml, or: "
+                f"sudo mkdir -p {ddir} && sudo chown $(id -un) {ddir}",
+            )
+        )
+
+    # Drift guard: castle.yaml is the single source of truth for the roots. An env var
+    # override is per-process, so it's the one way the CLI and the api service can still
+    # diverge (env set in your shell, absent in the service unit — the original bug).
+    for var in ("CASTLE_DATA_DIR", "CASTLE_REPOS_DIR"):
+        if var in os.environ:
+            checks.append(
+                Check(
+                    WARN,
+                    f"{var} overrides castle.yaml",
+                    detail=f"{var}={os.environ[var]}",
+                    hint=f"set data_dir:/repos_dir: in castle.yaml and unset {var}, so "
+                    "every process (CLI and api) resolves the same roots",
+                )
+            )
+
     missing = [n for n in (_GATEWAY, _API, _DASHBOARD) if not config.deployments_named(n)]
     if not missing:
         checks.append(Check(OK, "control plane registered", detail="gateway, api, dashboard"))