feat(genomic): add recursive boilerplate scanning

[pyramation]

Summary

Adds recursive boilerplate discovery to the genomic scaffolder, enabling proper filtering of directories that contain .boilerplate.json files. This solves the issue where non-boilerplate directories (like scripts/) would appear as options when using --dir . to bypass .boilerplates.json.

Key changes:

• New scanBoilerplatesRecursive function that recursively finds all directories with .boilerplate.json
• New findBoilerplateByPath function for matching user-provided paths against discovered boilerplates (exact match, then unambiguous basename match)
• Added scanBoilerplates method to TemplateScaffolder class for convenience
• Updated resolveFromPath to use recursive scanning as a fallback resolution strategy

With this change, when a user runs pgpm init --dir ., only directories with .boilerplate.json (e.g., default/module, default/workspace) will be available as options.

Review & Testing Checklist for Human

• Test with pgpm init: Clone pgpm-boilerplates and verify pgpm init --dir . only shows default/module and default/workspace, not scripts/
• Review basename matching logic in findBoilerplateByPath - returns null for ambiguous matches (e.g., if both default/module and supabase/module exist, module returns null)
• Performance check: The recursive scan is now called as a fallback in resolveFromPath. For large template repos, this could add latency. Consider if caching is needed.
• Consider adding unit tests for the new scanning functions before merging

Test Plan

1. Clone pgpm-boilerplates locally
2. Run pgpm init --dir . and verify only valid boilerplates appear
3. Run pgpm init module --dir . and verify it resolves to default/module
4. Verify normal pgpm init workspace still works (uses .boilerplates.json)

Notes

• The SKIP_DIRECTORIES list is hardcoded but can be extended via skipDirectories option
• No unit tests were added in this PR
• Link to Devin run: https://app.devin.ai/sessions/2015de005a8b4cb59e20b976c5d6696a
• Requested by: Dan Lynch (@pyramation)

[devin-ai-integration]

🤖 Devin AI Engineer

I'll be helping with this pull request! Here's what you should know:

✅ I will automatically:

• Address comments on this PR. Add '(aside)' to your comment to have me ignore it.
• Look at CI failures and help fix them

Note: I can only respond to comments from users who have write access to this repository.

⚙️ Control Options:

• Disable automatic comment and CI monitoring