CL-9386: runtime-denylist the active --config path holding skip

[TheGreatAxios]

Implements CL-9386 (warden finding on PR #1169): an operator-chosen --config path inside the workspace is model-readable/writable while carrying standing skip-permissions. The docs honestly disclosed this; now it is enforced.

Chosen shape

Runtime exact-path extras on the secret-guard plugin, not a warning and not a new static pattern:

• secretGuardPlugin({ extraDeniedPaths }) hard-denies path-keyed reads AND writes (both middleware loops), lexical + realpath legs (CL-6971 floor), even under --dangerously-skip-permissions — the active custom path is treated exactly like the default settings file. The static denylist is untouched (default machine-wide behavior unchanged and pinned by test).
• buildCorePosixToolPlugins({ secretGuardExtraDeniedPaths }) forwards it; TUI (session.ts) and exec (runner.ts) entry points pass [config.globalSettingsPath]; workers inherit it down the dispatch chain (tools.ts fleet deps → agent-fleet.ts nested dispatch + run params → run.ts).
• createCodexReadRawFile enforces the same list for apply_patch's Update-File raw-read leg, which bypasses the plugin middleware chain by design.
• Docs (ARCHITECTURE.md, IMPLEMENTATION.md, PRODUCT.md) move past disclosure into guarantee.

Deliberate non-goals (parity with the default file, not new systems): shell references to the custom path follow the existing permission gate (ask unless yolo) — under persisted yolo, shell can already show the default settings file, so this is at parity; @mention stays operator-consented per-read; content-search exfiltration of in-workspace secret files is a pre-existing accepted residual of the static guard and is unchanged.

Verification

• RED first: src/plugins/secret-guard-config-denylist.test.ts committed red (6 fail: custom config readable/writable in yolo+normal; 2 pins passed throughout).
• bun run typecheck — exit 0
• Targeted suites (secret-guard x5, posix-tool-plugins, apply-patch-diff, agent-fleet, config) — green
• Full bun test ./src ./tests ./evals ./scripts --randomize --seed 424242 — 8039 pass, 0 fail, exit 0
• bun run lint (oxfmt + oxlint) — exit 0

Related: PR #1169 (open) makes /yolo persist the active settings source, which is the live persistence path this protects; this PR is based on main and touches no #1169 code. Do not merge per dispatch (leave for review).

[github-actions]

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[linear-code]

CL-9386