fix: monorepo-aware setup commands and domain discovery improvements

[KyleAMathews]

Summary

• edit-package-json and add-library-bin now auto-detect monorepo roots and apply to all workspace packages that contain SKILL.md files, fixing the issue where only the root package.json was modified
• Domain discovery skill now reads all in-repo docs before interviewing and distinguishes factual questions (search the codebase) from judgment questions (ask the maintainer)

Root Cause

When a library maintainer ran npx @tanstack/intent edit-package-json from a monorepo root, the command operated on process.cwd() only — modifying the root package.json instead of each workspace package's package.json. This meant "skills" and "bin" were never added to the individual packages, so npm publish excluded the skills directories entirely.

Separately, the domain-discovery skill's hard rules enforced interactive interviews so strictly that the agent would ask factual questions ("are there other backward compat middlewares?") instead of just grepping the codebase. And Phase 1 only read README + quickstart, not the full in-repo docs, so the agent lacked context it could have gathered autonomously.

Approach

Monorepo resolution (setup.ts):

• readWorkspacePatterns() — reads workspace globs from pnpm-workspace.yaml or package.json workspaces
• resolveWorkspacePackages() — resolves glob patterns (packages/*, packages/**) to actual package directories
• findPackagesWithSkills() — filters to packages containing at least one SKILL.md file
• runForEachPackage<T>() — generic wrapper that runs a command on each matching package, with proper fallback semantics

Key invariant: if workspace config is detected but no packages have skills, the command warns and returns empty — it never falls through to modify the monorepo root's package.json.

Domain discovery (SKILL.md):

• New hard rule Feedback on using "skill-tree-generator" #3: factual questions must be answered by searching code; only judgment questions go to the maintainer
• Phase 1a item Rewrite domain-discovery to v3.0: task-focused skills, new phase ordering #5: read all in-repo .md files before the first interview

Non-goals

• Did not add monorepo awareness to setup-github-actions (it operates on the repo root by design)
• Did not change the validate command (it already accepts a directory argument)

Trade-offs

The workspace glob resolution is a simple readdirSync-based implementation rather than using a full glob library. This handles the common patterns (packages/*, examples/**/*) but won't handle complex globs like packages/{foo,bar}. This covers the vast majority of real monorepo layouts; a full glob library can be added later if needed.

Verification

cd packages/intent && pnpm run build && pnpm test:lib
# 133 tests pass (6 new for monorepo-aware commands)

Files changed

File	Change
meta/domain-discovery/SKILL.md	New hard rule #3 (search before asking), Phase 1a item #5 (read all in-repo docs)
src/cli.ts	Swap single-package imports to monorepo-aware *All variants
src/setup.ts	Add workspace resolution, MonorepoResult<T>, runForEachPackage<T>, error handling
tests/setup.test.ts	6 new tests: pnpm workspace, package.json workspace, single-package fallback, empty monorepo warning, bin generation

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