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>

install.sh

@@ -279,6 +279,19 @@ create_directories() {
         printf 'gateway:\n  port: 9000\n' > "${CASTLE_HOME}/castle.yaml"
         log_ok "seeded ~/.castle/castle.yaml"
     fi
+
+    # Persist the chosen roots into castle.yaml so every later `castle` (CLI, in the
+    # shell) and `castle-api` (service) invocation resolves the SAME dirs from the file
+    # — not from a per-process env var that only one of them happens to have. Only when
+    # non-default, to keep the file minimal; idempotent (grep-guarded), like repo: below.
+    if [ "${DATA_DIR}" != "/data/castle" ]; then
+        grep -q "^data_dir:" "${CASTLE_HOME}/castle.yaml" 2>/dev/null \
+            || printf 'data_dir: %s\n' "${DATA_DIR}" >> "${CASTLE_HOME}/castle.yaml"
+    fi
+    if [ "${REPOS_DIR}" != "/data/repos" ]; then
+        grep -q "^repos_dir:" "${CASTLE_HOME}/castle.yaml" 2>/dev/null \
+            || printf 'repos_dir: %s\n' "${REPOS_DIR}" >> "${CASTLE_HOME}/castle.yaml"
+    fi
 }
 
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