fix(config): trust the invoking project, and stop leaking what it must not decide

Review found five real defects in the configuration-source work, all confirmed
against the code rather than argued:

1. The note claimed --config outranks settings.yaml. It does not: the settings
   seam registers a plugin's cordis entry config as the `base` layer and the
   user section layers over it, and the seam cannot tell a shipped value from a
   --config one. The note now states shipped reality and names --config-replace
   as the lever for a deployment that must win. Separately, a literal `apiKey`
   in settings outranked both the environment and .credentials.yaml — the field
   is removed, so configuration carries a reference and nothing else.
2. DEEPSEEK_SEARCH_BASE_URL was functionally deleted: the shipped inline went
   away without the provider learning to read it. It now resolves from the
   environment snapshot, as the README always claimed.
3. The bootstrap deny list missed the interpreter start-up hooks. BASH_ENV is
   the sharpest: `bash -c` sources it on every bash tool call, so a project
   .env could run a file of its choosing before every command. The list now
   covers BASH_ENV and its per-language siblings, the Git hook commands, and
   the remaining preload and CA variables, organised by what a variable does
   rather than which runtime owns it.
4. YAML parse errors quoted the offending source line — which in a credentials
   document is the secret — into boot stderr and the watcher's logger. Only the
   error code and position are reported now, in credentials-local and
   settings-local alike, pinned by a test that asserts the secret is absent.
5. 0600 governed only files the harness wrote. A hand-created 0644 document was
   read normally. POSIX now checks the mode before reading contents, at boot
   and on every reload; Windows has no mode to inspect and is skipped rather
   than faked.

The project a session is launched in is trusted by default, with no prompt and
no stored trust record: it may supply its own endpoint, ordinary variables, and
a key ranked below the managed store. Trust stops at the harness itself — a
discovered file still cannot set DSH_PERMISSION_MODE, PATH, BASH_ENV, or the
rest, because those take effect with no user action, before any turn, outside
the permission policy and the sandbox.

examples/headless-agent/tests/fixtures/deepseek-defaults.cordis.yml

@@ -5,7 +5,6 @@
     patches:
       - id: llm-deepseek
         config:
-          apiKey: snapshot-key
           baseURL: !!js process.env.DSH_SNAPSHOT_BASE_URL
           thinking: disabled
       - id: cli-agent

examples/headless-agent/tests/headless.snapshot.ts

@@ -244,13 +244,12 @@ describe('headless stream-json snapshots', () => {
       prepare: (cwd) => { runCwd = cwd },
     })
 
-    // The guidance leads with the credential store — the path that keeps the
-    // secret out of configuration files — and offers a literal key last.
+    // The guidance names both places a credential can come from, and nothing
+    // else: configuration carries the reference, never a literal key.
     expect(result.stderr).toBe(
       'dsh-cli-demo: turn 1 failed at step 1: llm-deepseek: no API key for provider route "deepseek-official";'
       + ' store DEEPSEEK_API_KEY through the credentials service (the web Models page writes it),'
-      + ' export DEEPSEEK_API_KEY in the launching environment, or — as a last resort — set a literal'
-      + ' "apiKey" in the llm-deepseek settings section\n',
+      + ' or export DEEPSEEK_API_KEY in the launching environment\n',
     )
     const normalized = normalizeHeadlessStream(result.stdout, runCwd)
     if (refreshing) await writeFile(streamExpected, normalized)
@@ -314,6 +313,9 @@ describe('headless stream-json snapshots', () => {
         ],
         tsconfigPath,
         env: {
+          // Configuration carries only the reference; the key rides the
+          // launching environment, which is the whole credential plane here.
+          DEEPSEEK_API_KEY: 'snapshot-key',
           DSH_SNAPSHOT_BASE_URL: server.url,
           NODE_OPTIONS: [process.env.NODE_OPTIONS, '--disable-warning=ExperimentalWarning'].filter(Boolean).join(' '),
         },

examples/headless-agent/tests/snapshots/missing-credential/stream-json.expected.jsonl

@@ -5,5 +5,5 @@
 {"type":"session_event","sessionId":"{{sessionId}}","event":{"type":"request/header","seq":4,"time":0,"data":{"header":{"config":{"provider":"deepseek-official","model":"deepseek-v4-flash","maxTokens":256000,"reasoningEffort":"high"},"adapterDefaults":{"reasoningEffort":true,"maxTokens":true},"system":"{{system}}","tools":"{{tools}}"},"reason":"initial"}}}
 {"type":"session_event","sessionId":"{{sessionId}}","event":{"type":"request/context","seq":5,"time":0,"data":{"provider":"deepseek-official","model":"deepseek-v4-flash","contextWindow":1000000}}}
 {"type":"session_event","sessionId":"{{sessionId}}","event":{"type":"step/end","seq":6,"time":0,"data":{"turn":1,"step":1}}}
-{"type":"session_event","sessionId":"{{sessionId}}","event":{"type":"turn/end","seq":7,"time":0,"data":{"turn":1,"reason":{"kind":"error","step":1,"failure":{"message":"llm-deepseek: no API key for provider route \"deepseek-official\"; store DEEPSEEK_API_KEY through the credentials service (the web Models page writes it), export DEEPSEEK_API_KEY in the launching environment, or — as a last resort — set a literal \"apiKey\" in the llm-deepseek settings section","code":"MISSING_CREDENTIAL"}}}}}
-{"type":"result","success":false,"sessionId":"{{sessionId}}","turn":1,"result":"","reason":{"kind":"error","step":1,"failure":{"message":"llm-deepseek: no API key for provider route \"deepseek-official\"; store DEEPSEEK_API_KEY through the credentials service (the web Models page writes it), export DEEPSEEK_API_KEY in the launching environment, or — as a last resort — set a literal \"apiKey\" in the llm-deepseek settings section","code":"MISSING_CREDENTIAL"}}}
+{"type":"session_event","sessionId":"{{sessionId}}","event":{"type":"turn/end","seq":7,"time":0,"data":{"turn":1,"reason":{"kind":"error","step":1,"failure":{"message":"llm-deepseek: no API key for provider route \"deepseek-official\"; store DEEPSEEK_API_KEY through the credentials service (the web Models page writes it), or export DEEPSEEK_API_KEY in the launching environment","code":"MISSING_CREDENTIAL"}}}}}
+{"type":"result","success":false,"sessionId":"{{sessionId}}","turn":1,"result":"","reason":{"kind":"error","step":1,"failure":{"message":"llm-deepseek: no API key for provider route \"deepseek-official\"; store DEEPSEEK_API_KEY through the credentials service (the web Models page writes it), or export DEEPSEEK_API_KEY in the launching environment","code":"MISSING_CREDENTIAL"}}}