FE-881: Cook agent loads the target repo's sandbox-scoped skills

[kostandinang]

Stack Context

Stacks on FE-864 (#224). A refinement of cook-codebase-mode + the cook-time grounding direction (D160-K intact -- this is run-time, not the emitter). FE-881.

What?

• cookResourceLoader(sandboxDir, agentDir, systemPrompt) -- points pi's discovery at the repo's .agents/skills / .claude/skills (deduped by realpath, since brunch-style repos symlink the two), then filters the result to paths under the sandbox via sandboxScopedSkills. pi's default discovery scans <cwd>/<config>/skills + <agentDir>/skills, not the Agent-Skills dirs, so the explicit additionalSkillPaths are required.
• sandboxScopedSkills(skills, sandboxDir) -- pure filter: keeps only skills whose path resolves under the sandbox; drops global, sibling-slice, and prefix-lookalike paths.
• The catalog reaches the model through pi's custom-prompt path (formatSkillsForPrompt, gated on the read tool -- every cook action has it), so the task-prompt override does not suppress it.

Why?

Brownfield cook builds on the user's repo, so the agent should see that repo's own skills and conventions. buildSessionOptions previously stripped all skills for hermeticity. This narrows the guarantee from "no skills" to "no skills from outside the repo" -- the cook agent gains the target codebase's configured skills while the developer's machine-global pi config still never leaks in.

Behavior / scope

• Greenfield worktrees have no .agents/skills, so skills resolve empty and greenfield behavior is unchanged (protecting invariant).
• Deferred follow-ons (separate slices): loading the repo's AGENTS.md/CLAUDE.md conventions; a project-trust gate for repo-authored skills.

Tests

npm run verify green (2060 passed, 2 skipped, build OK). New unit test pins sandboxScopedSkills (under / sibling / prefix-lookalike / global); new fs-integration test pins cookResourceLoader discovering the repo's .agents/skills and excluding an agentDir (global) skill.

[kostandinang]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

• FE-883: Cook artifact lifecycle — git-merge slice composition #230
• FE-881: Cook agent loads the target repo's sandbox-scoped skills #227 👈 (View in Graphite)
• FE-883: Cook operational hardening — runtime stability, agent skills, git-merge composition, run GC #224 : 1 other dependent PR (#232 )
• FE-864: Brownfield feature delivery from spec — detect, classify, probe, oracle, promote, serve #212 : 2 other dependent PRs (#213 , #223 )
• FE-841: Pi agent foundations — in-process SDK, toolchain profiles #194 : 2 other dependent PRs (#198 , #211 )
• main

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PR Summary

Medium Risk
Loading repo-authored skills increases what the agent executes during brownfield cooks (trust boundary), though global skills remain excluded; remaining changes are UI/CLI and filesystem edge cases.

Overview
Brownfield cook agents now see skills from the target repo’s .agents/skills / .claude/skills (deduped by realpath), filtered by sandboxScopedSkills so machine-global, sibling-slice, and prefix-lookalike paths never load. Session setup uses cookResourceLoader instead of stripping all skills; greenfield worktrees without those dirs stay unchanged.

Presenter / CLI: plate advances only on lines matching ✓ promoted, not incidental “promoted” text (e.g. “nothing promoted”). Promotion failures emit cook-done with ok: false and a reason before exit.

Other: Activity heartbeat tail truncation counts the ellipsis in the 56-char cap; runPi defers creating the isolated agent dir until after timeout setup; Windows directory symlinks in copyMissingTopLevelEntries use junctions when needed.

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