fix(config): close the review findings on configuration source ownership

Two had real security consequences:

The bootstrap rejection ran on npm dotenv's parser while process.loadEnvFile
applied the file with Node's own. Two independently maintained dialects meant
the check and the thing it guards could disagree: a name Node accepts but the
checker misses would reach process.env unchecked, and BASH_ENV there runs a
file of the project's choosing on every `bash -c` the bash tool issues. Parse
once with node:util's parseEnv — the same engine loadEnvFile uses — and assign
the entries already checked, which also drops the dotenv dependency.

llm-pi-ai still returned a literal profile.apiKey ahead of everything, and it
registers a settings namespace, so the defect removed from llm-deepseek
survived intact in its design twin. The field is gone from the profile schema,
the resolution path, and the tests.

The rest are consistency and documentation defects the review named:

- verify-config-source-ownership did not scan the Python runtime's bundled
  cordis.yml, which still inlined apiKey and baseURL. Both are covered now, and
  the line-anchored INLINE_DENY documents that it is a tripwire, not a parser.
- The deny list missed NODE_TLS_REJECT_UNAUTHORIZED, the askpass hooks, the
  GIT_CONFIG_* redirections, and PYTHONHOME — all implied by its own stated
  rule about what a variable does.
- Snapshot lookups folded case on Windows, where environment names are
  case-insensitive and an exact-match Map could miss a higher-ranked layer.
- The credentials note claimed a read-time permission check was "not taken"
  while this PR implemented it; the credentials-local README still described
  two layers, live process.env reads, dotenv-era limitations, and a renamed
  anchor; the llm-deepseek README still advertised the removed literal apiKey;
  and web.ts and base.cordis.yml kept personal-overlay wording.
- The ownership note's literal-apiKey claim now names its scope: the
  web-search providers keep a literal field but register no settings
  namespace, so nothing can shadow a stored credential through them.

.agents/notes/implemented/architecture/2026-08-04-configuration-source-ownership.md

@@ -56,7 +56,7 @@ The line is that these take effect with no user action, before any turn, outside
 - A `.env` holding `DSH_*`, `PATH`, or a proxy variable fails the launch instead of being applied. Developers keeping switches in a repository `.env` move them to their shell — a deliberate, loud break.
 - `--config` is no longer overridable by a stale shell endpoint. It is still overridable by a user's stored `settings.yaml`, which is the settings seam's layering and not something this note changes; a deployment that must win against stored settings uses `--config-replace`.
 - Not solved: the layers are still materialized into `process.env`, so ordinary project variables continue to reach child processes under the subprocess scrub. Bootstrap variables cannot come from a file at all, which closes the escalation path; a project `.env` setting something like `GIT_SSH_COMMAND` for the tools an agent runs remains possible and is recorded as a limitation on the package.
-- The adapters no longer accept a literal `apiKey`: configuration carries the reference and nothing else, so a settings document cannot become a second credential store. No adapter namespace is strict, so writing one is dropped rather than rejected.
+- The LLM adapters no longer accept a literal `apiKey`: configuration carries the reference and nothing else, so a settings document cannot become a second credential store. No adapter namespace is strict, so writing one is dropped rather than rejected. The web-search providers still declare a `role('secret')` literal key; they register no settings namespace, so nothing can shadow a stored credential through them, but the claim is about the adapters rather than the repository as a whole.
 - Exa and Perplexity still capture their key at load time rather than through the credential seam. They no longer read raw `process.env` — they resolve through the trusted layers — but converting them to per-request seam resolution is separate work.
 
 ## Alternatives considered