fix(workspace): discover worktrees nested in boundary dirs

[jahvon]

Summary

Dynamic workspace discovery walks past a flow.yaml found under .claude, vendor, third_party, and similar directories inside a registered workspace, so a vendored copy never becomes the workspace. Agent tools put worktrees inside the repo (Claude Code uses <repo>/.claude/worktrees/<name>), so commands run in those worktrees resolved to the registered main checkout and ran its executables instead of the worktree's.

The boundary now exempts linked git worktrees, detected by a .git file whose gitdir contains a commondir. The check doesn't depend on where a tool places its worktrees. Submodules also have a .git file but no commondir, so a vendored submodule stays excluded.

Notable Changes

• discoveryBoundary accepts any linked-worktree root
• Resolver specs for a worktree under .claude/worktrees and a submodule under vendor

No ticket

[jahvon]

Verification

• flow validate passed: generate, lint, unit and e2e tests, schema check
• Manually: built ./bin/flow and ran flow workspace get in a real Claude Code worktree (tuikit/.claude/worktrees/pin-golangci-lint). v2.3.0 resolved it to the main tuikit checkout; this build resolves it to the worktree. The main checkout still resolves to tuikit.
• Not verified: the generated-diff step reported "Skipping diff validation" locally, so CI's validate generated is the first real run of that check. No generated files are touched. Windows wasn't exercised; isLinkedWorktree uses filepath throughout.

Worth a close look

• pkg/filesystem/resolve.go isLinkedWorktree: the commondir heuristic for telling a worktree from a submodule

Out of scope (follow-up)

• An unregistered worktree is named after its folder, not the workspace it came from, so a self-qualified ref (tuikit/ns:x) inside a worktree still goes to the registered checkout. None of the current workspaces use self-qualified refs; revisit if someone reports one.

[codecov]

Codecov Report

❌ Patch coverage is 85.71429% with 2 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
pkg/filesystem/resolve.go	85.71%	1 Missing and 1 partial ⚠️

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