fix(cli): align ensureCheckout with PM-unified store layout

[amondnet]

Summary

• ensureCheckout returned the legacy github/checkouts/<owner>__<repo>/<ref>/ path while GithubSource.fetch writes to the PM-unified github/github.com/<owner>/<repo>/<tag>/ layout.
• The mismatch made ask docs github:<owner>/<repo> and ask src … exit 0 with no output after a successful fetch — callers walked a non-existent directory and findDocLikePaths returned [].
• Fixed by switching ensureCheckout to githubStorePath(askHome, 'github.com', owner, repo, ref) so the lazy and eager pipelines agree on the exact same path.

Changes

• packages/cli/src/commands/ensure-checkout.ts — use githubStorePath instead of legacy checkouts/ path
• packages/cli/test/commands/ensure-checkout.integration.test.ts — new integration test that mocks the real fetch by writing to the PM-unified layout and asserts ensureCheckout + runDocs both land on the same existing path
• packages/cli/test/commands/ensure-checkout.test.ts, cache-sharing.test.ts, src.test.ts — updated to use the PM-unified layout in fixtures and structural assertions

Test Plan

• bun run --cwd packages/cli test test/commands/ → 57/57 pass
• Manual: ask docs github:agentskills/agentskills now prints the checkout root and /docs subdir instead of emitting nothing

---

Summary by cubic

Aligns the CLI checkout path with the PM‑unified GitHub store layout and returns the fetcher’s actual store path when a fallback ref wins, so ask docs/ask src read the real directory and no longer emit empty output. ensureCheckout now resolves to ~/.ask/github/github.com/<owner>/<repo>/<ref>/ or the fetcher-reported storePath.

• Bug Fixes
  • Switched to githubStorePath(askHome, 'github.com', owner, repo, ref) and prefer FetchResult.storePath when present to fix both naming and ref-candidate divergence.
  • Added integration tests pinning ensureCheckout ↔ GithubSource.fetch ↔ runDocs path agreement (including fallback-ref winner); updated unit tests and fixtures to the PM‑unified layout.

^{Written for commit 9f25e8f. Summary will update on new commits.}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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[cubic-dev-ai]

No issues found across 5 files

_{Auto-approved: Aligns checkout paths with the unified store layout to fix a bug causing silent failures. Low-risk logic change with comprehensive integration and unit test coverage.}

Architecture diagram

sequenceDiagram
    participant User
    participant CLI as CLI (docs/src command)
    participant EC as ensureCheckout
    participant GS as GithubSource
    participant FS as Local Store (~/.ask/github/)
    participant GH as GitHub API

    User->>CLI: run "ask docs github:owner/repo"
    CLI->>EC: ensureCheckout(spec)

    Note over EC,FS: PATH RESOLUTION
    EC->>EC: CHANGED: Compute checkoutDir using githubStorePath<br/>(github.com/owner/repo/ref)
    
    EC->>FS: Check if directory exists
    
    alt Cache Hit (Path Exists)
        FS-->>EC: Directory found
    else Cache Miss (Path Missing)
        EC->>GS: fetch(repo, ref)
        GS->>GH: Download repository source
        GH-->>GS: Source Data
        GS->>FS: CHANGED: Write to PM-unified layout<br/>(github.com/owner/repo/ref)
        FS-->>GS: Success
        GS-->>EC: Return storePath
    end

    EC-->>CLI: Return checkoutDir (Absolute Path)

    Note over CLI,FS: CONTENT DISCOVERY
    CLI->>CLI: findDocLikePaths(checkoutDir)
    CLI->>FS: Read directory content at checkoutDir
    
    alt Path Alignment Success (NEW)
        FS-->>CLI: File list (README, /docs, etc.)
        CLI->>User: Print documentation paths
    else Path Mismatch (Legacy Bug)
        Note over CLI,FS: Legacy path (checkouts/owner__repo) != Unified path
        FS-->>CLI: Error / Directory Not Found
        CLI->>User: Exit 0 (Silent - No Output)
    end

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[cubic-dev-ai]

0 issues found across 4 files (changes from recent commits).

_{Requires human review: Aligning checkout paths with the PM-unified layout involves architectural context and impacts how CLI commands locate files, which warrants human verification.}