Keep pending BOOTSTRAP.md and bootstrap truncation notices in system-prompt Project Context instead of WebChat/runtime user context. Preserve bootstrap instructions when systemPromptOverride is configured.
Add inline docker build commands for npm-installed users who don't have the
source checkout scripts. Update all docs referencing sandbox-setup.sh,
sandbox-common-setup.sh and sandbox-browser-setup.sh to note they are
source-checkout-only and link to the new inline instructions.
Fixes#75485.
Adds `agents.defaults.skipOptionalBootstrapFiles` for optional workspace bootstrap files, validates the supported filenames, and propagates the option through workspace bootstrap callers.
Also preserves legacy setup detection when `USER.md` or `IDENTITY.md` are intentionally skipped, documents the config field, and includes focused regression coverage.
Landing follow-up included small CI unblockers for current-base drift: removing an unused Brave runtime dependency, fixing Telegram RTT lint, and preserving compatible gateway-bindable plugin registry cache reuse when runtime ensures disable bundled dependency installation.
Add reasoningDefault support under agents.defaults and preserve the existing per-agent/session/inline override order.
Includes authorization gating for configured reasoning state, /status coverage, config schema/docs baseline updates, and regression tests for the reply and status paths. Also carries the related cron startup-run preservation fix and CI test stabilization needed for this PR branch.
Validated locally with pnpm check:changed, the focused Vitest bundle for touched gateway/cron/auto-reply/plugin-sdk/tooling tests, pnpm config:docs:check, and git diff --check. GitHub checks are green on the merged head; Greptile latest visible review is 4/5 with no P0/P1 findings.
Two recent code changes lacked or had only partial doc coverage:
- contextInjection 'never' (#65006, xDarkicex): the new mode is now
documented under agents.defaults.contextInjection, alongside the
existing 'continuation-skip' mode, with guidance on when to use it
(custom context engines, native runtimes that own their prompt).
- Nix Home Manager daemon PATH (#44402, jerome.benoit): document the
service PATH auto-discovery (NIX_PROFILES right-to-left precedence
and ~/.nix-profile/bin fallback) under the Nix install page.
Also sentence-case three Title-Cased headings on the Nix page ('What
You Get', 'Quick Start', 'Nix Mode Runtime Behavior') and drop a
duplicate body H1 that restated the frontmatter title.
