fix(cli): strip removed library from AGENTS.md on ask remove

[amondnet]

Summary

• Fix ask remove leaving the removed library's section (or the whole auto-generated block) in AGENTS.md when the last entry is removed from ask.json
• runInstall now regenerates AGENTS.md even when the full install has zero targets (previously short-circuited without touching the file)
• generateAgentsMd now strips the existing <!-- BEGIN:ask-docs-auto-generated --> … <!-- END --> block on empty input: deletes AGENTS.md when only the block remained, preserves user-authored content otherwise
• Added 3 CLI-level tests covering non-last removal, last-library removal (file deleted), and user content preservation

Root cause

Two cooperating early returns skipped regeneration when askJson.libraries became empty:

1. runInstall short-circuited on targets.length === 0 before calling generateAgentsMd
2. generateAgentsMd returned '' on libraries.length === 0 without touching AGENTS.md

The happy path (remove a non-last library) worked because runInstall still hit the regeneration call with the remaining libraries.

Test plan

• bun run --cwd packages/cli test test/install/remove.test.ts — 4 pass
• bun run --cwd packages/cli test — 473 pass / 0 fail
• bun run --cwd packages/cli lint — clean
• bun run --cwd packages/cli build — typecheck clean

Follow-up (not in this PR)

ask remove still does not call removeFromIntentSkillsBlock, so intent-format packages leave their <!-- intent-skills:start --> entries behind. Tracked for a separate PR.

---

Summary by cubic

Fixes ask remove leaving stale entries in AGENTS.md, ensures the file is cleaned when the last library is removed, and warns on orphaned markers to prevent silent corruption.

• Bug Fixes
  • generateAgentsMd: on empty input, strips the auto-generated block; deletes AGENTS.md if only the block remained; preserves user content; logs a consola.warn and leaves the file untouched when markers are mismatched.
  • runInstall: when not scoped with --only-specs and targets are empty, regenerates AGENTS.md and updates ignore files; when scoped and no specs match, skips regeneration.
  • Added CLI tests for removing a single library, removing the last library (file deleted), preserving user content before/after the block, orphan marker warning (BEGIN or END), and the --only-specs no-match case.

^{Written for commit 1675e4e. Summary will update on new commits.}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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View logs

[cubic-dev-ai]

No issues found across 3 files

_{Requires human review: Modifies core CLI logic and handles file deletions based on manual string parsing of project files. This logic change in a core path warrants human review to ensure no data loss edge cases.}

Architecture diagram

sequenceDiagram
    participant User
    participant CLI as CLI Engine
    participant Install as runInstall()
    participant Agents as generateAgentsMd()
    participant FS as File System (AGENTS.md)
    participant Ignore as manageIgnoreFiles()

    User->>CLI: ask remove [library]
    CLI->>FS: Update ask.json
    CLI->>Install: sync state

    Note over Install,FS: Handling Last Library Removal

    alt targets.length == 0
        Install->>Install: Detect empty targets
        
        rect rgb(240, 240, 240)
            Note right of Install: CHANGED: Previously short-circuited here
            Install->>Agents: NEW: generateAgentsMd(projectDir, [])
            
            Agents->>FS: Check if AGENTS.md exists
            opt File exists
                Agents->>FS: Read AGENTS.md content
                Agents->>Agents: NEW: Strip <!-- BEGIN/END --> block
                
                alt Only auto-generated block existed
                    Agents->>FS: NEW: Delete AGENTS.md (fs.rmSync)
                else User-authored content remains
                    Agents->>FS: NEW: Overwrite AGENTS.md (fs.writeFileSync)
                end
            end
            Agents-->>Install: return empty string
        end

        Install->>Ignore: NEW: manageIgnoreFiles(projectDir, 'remove')
    else targets.length > 0
        Install->>Install: Resolve remaining libraries
        Install->>Agents: generateAgentsMd(projectDir, libraries)
        Agents->>FS: Update AGENTS.md block
        Install->>Ignore: manageIgnoreFiles(projectDir, 'add')
    end

    Install-->>CLI: Return summary
    CLI-->>User: Operation complete

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[cubic-dev-ai]

0 issues found across 2 files (changes from recent commits).

_{Auto-approved: Safe bug fix for CLI documentation maintenance; correctly handles AGENTS.md cleanup and adds comprehensive tests.}

[cubic-dev-ai]

0 issues found across 1 file (changes from recent commits).

_{Auto-approved: Fixes cleanup logic in AGENTS.md when libraries are removed. Includes comprehensive tests and defensive handling of user-authored content.}