Contain linked project skill roots inside the repository

[ylcn91]

Human comments

What was wrong

scanSkillRootFiles opened a non-recursive project skill root before
resolving it against the workspace boundary, so a root that is itself a
symlink was scanned wherever it pointed. A checked-in .claude/skills
link to a directory outside the repository put every skill under it into
the project's skill and command lists, with origin: "project". The
recursive shape already resolved the same plumbed boundaryPath before
walking, and docs/provider-plugin-api.md already states the rule for
both shapes: a symlink out of a project root is followed within the
workspace for a plain root and within the repository root for a root
that walks ancestors or that the plugin resolved.

Issue: #2769. Investigation report: https://get-bb.github.io/reports/issues/2769.html

What changed

resolveRecursiveRootPath becomes resolveBoundedRootPath and the flat
skill root scan consults it, so both shapes enforce one containment rule
against the same boundaryPath. A root link that stays inside the
repository still resolves and is still scanned, and user-origin roots,
which carry no boundary, are unaffected.

No field or message on the server/host-daemon wire changed, so
HOST_DAEMON_PROTOCOL_VERSION stays at 178.

How you verified

• Added two command-discovery regressions: a project .claude/skills
  root symlinked outside the workspace discovers nothing, and one
  symlinked to .agents/skills inside the workspace still discovers its
  skill. The first fails on the parent commit
  (expected [ { name: 'leaked', …(4) } ] to deeply equal []) and
  passes here; the second passes on both.
• pnpm exec turbo run test --filter=@bb/host-daemon --force: 46 files,
  574 tests passed (1 failed before the fix).
• pnpm exec turbo run typecheck --filter=@bb/host-daemon: passed.
• BB_TEST_TIMEOUT_SCALE=3 pnpm exec turbo run test --filter=@bb/integration-tests --force --env-mode=loose -- native-roots-golden: 22 provider golden fixtures passed unchanged,
  including the cursor symlink-boundary and grok symlink variants.
• Drove listHostCommands with the shipping claude-code declaration
  (.claude/skills, ancestors: true) over the issue's fixture: the
  escaping root reported ["leaked"] before and [] after, while the
  in-repository link reported ["in-repo"] in both.

Fixes #2769

AGENT GENERATED