Support extra front matter, flat skill structure

[dacharyc]

Add support for extra frontmatter in the form of an optional --allow-extra-frontmatter flag. The flag suppresses warnings on frontmatter fields that are non-spec-compliant; for example, the Claude Code-supported user-invokable field. Requested in #27 . Preserves default behavior of warning on non-spec-compliant frontmatter fields, but provides an escape hatch for folks who are developing for a specific platform and don't want warnings.

Also adds support for flat layouts in the form of an optional --allow-flat-layouts flag. With this flag:

• Structure warnings: Root-level files alongside SKILL.md no longer trigger extraneous file warnings. Unknown directory warnings are unaffected.
• Token counting: Root-level text files are counted as standard content (with the same per-file and aggregate thresholds as references/ files) instead of "other" files. This also prevents the "not structured as a skill" ratio check from false-positiving on flat layouts.
• Orphan detection: Root-level files are checked for references in SKILL.md. Unreferenced files are flagged as potential orphans.

Default behavior is unchanged when the flag is not set.

[philoserf]

The title seems like #23 but the text speaks only of frontmatter.

[dacharyc]

The title seems like #23 but the text speaks only of frontmatter.

Yup, you're right, @philoserf - I implemented the simpler one first as a pattern for the --allow-flat-layouts flag, which has a few more behavior changes than the simpler one.

Does this meet your needs as communicated in #23 ?

[philoserf]

I'll test it and comment there.