feat: Add Codex skill support and restore Bun workflows

[jan-kubica]

What changed

This branch adds the repo's Codex/AI command and skill wiring, including the shared AI submodule integration, generated skill layouts for Claude and Codex, contributor documentation updates, and the new link-codex helper script.

It also fixes a manifest regression introduced during that work: package.json had ended up with two scripts objects. Bun only surfaced the first one, which broke bun run lint, bun run typecheck, bun run build, and the prepublishOnly release path.

Why

The branch is meant to make the repo's AI helper workflow reproducible for contributors using both Claude-style commands and Codex-style skills. While reviewing the repo state, the duplicate scripts key showed up as a blocker because it made the documented Bun workflow and the Bun-driven publish path unreliable.

Impact

Contributors can now use the documented Bun commands again.

CI/build tooling that depends on bun run can resolve the expected scripts.

The Codex skill sync/link workflow stays available without shadowing the rest of the package automation.

Root cause

The new Codex helper scripts were added in a second top-level scripts block instead of being merged into the existing one. JSON accepts the duplicate key, but Bun did not behave like npm here, so the broken state was easy to miss unless you exercised the Bun-native commands directly.

Validation

• bun run lint
• bun run typecheck
• bun test
• bun run prepublishOnly

---

[greptile-apps]

Greptile Summary

This PR does two things: it wires up Codex/AI skill tooling (shared submodule bump, skill directory restructure, new link-codex wrapper script, and contributor docs) and fixes a package.json regression where a second scripts block was silently shadowing the first under Bun, breaking lint, typecheck, build, and the prepublishOnly release path. It also upgrades tsdown from ^0.12.4 to ^0.21.6 and adds fixedExtension: false to tsdown.config.ts to preserve the .js/.d.ts output extension convention that the existing package.json export map depends on.\n\nKey changes:\n- Bug fix: Duplicate scripts key in package.json collapsed into a single canonical block; link-codex script entry added.\n- Tooling: tsdown bumped to ^0.21.6; fixedExtension: false set in config to prevent extension drift breaking the export map.\n- Scripts: scripts/link-codex-skills.sh added with two-stage guard (submodule present + target file exists); scripts/sync-ai-skills.sh upgraded with the same improved guard pattern.\n- Docs: CONTRIBUTING.md gains sync layout diagram and bun run link-codex usage instructions.\n- Restructure: .agents/skills/*.md files moved into per-skill subdirectories as SKILL.md to match Codex's expected layout.

Confidence Score: 5/5

Safe to merge; no blocking issues found across any of the changed files.

All changes are well-scoped and the critical package.json fix is straightforward. The tsdown upgrade is significant in version number but is handled correctly with fixedExtension: false, and the author validated the full build + publish path. The new scripts follow the same guard pattern as the existing ones and delegate safely to the shared submodule. No P0 or P1 issues found.

No files require special attention.

Important Files Changed

Filename	Overview
package.json	Merges duplicate scripts blocks into one and adds link-codex entry; bumps tsdown devDependency from ^0.12.4 to ^0.21.6.
tsdown.config.ts	Adds fixedExtension: false to keep .js/.d.ts output extensions aligned with package.json exports after the tsdown 0.21 upgrade.
scripts/link-codex-skills.sh	New wrapper script with two-stage guard (submodule directory presence + target file existence) before delegating to the shared submodule script.
scripts/sync-ai-skills.sh	Improved guard logic: now checks for directory existence and non-empty state before checking for the target file, with clearer error messages for each case.
CONTRIBUTING.md	Adds sync layout diagram, bun run link-codex documentation, and clarifies CODEX_SKILL_PREFIX usage.
bun.lock	Lock file regenerated for the tsdown ^0.12.4 → ^0.21.6 bump; pulls in @babel/generator@8.0.0-rc.3 and related transitive dependencies as part of the new rolldown-plugin-dts dependency tree.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A["bun run sync-ai"] --> B["scripts/sync-ai-skills.sh"]
    B --> C{".ai/shared dir\npresent & non-empty?"}
    C -- No --> D["exit 1\n(submodule not init'd)"]
    C -- Yes --> E{".ai/shared/scripts/\nsync-ai-skills.sh exists?"}
    E -- No --> F["exit 1\n(incompatible submodule)"]
    E -- Yes --> G["bash .ai/shared/scripts/sync-ai-skills.sh ."]
    G --> H[".claude/commands/skill.md"]
    G --> I[".agents/skills/skill/SKILL.md"]

    J["bun run link-codex"] --> K["scripts/link-codex-skills.sh"]
    K --> L{".ai/shared dir\npresent & non-empty?"}
    L -- No --> M["exit 1\n(submodule not init'd)"]
    L -- Yes --> N{".ai/shared/scripts/\nlink-codex-skills.sh exists?"}
    N -- No --> O["exit 1\n(incompatible submodule)"]
    N -- Yes --> P["bash .ai/shared/scripts/link-codex-skills.sh ."]
    P --> Q["CODEX_HOME/skills/stdnum-skill -> SKILL.md"]

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[devin-ai-integration]

✅ Devin Review: No Issues Found

Devin Review analyzed this PR and found no potential bugs to report.

View in Devin Review to see 2 additional findings.