fix(audit-scan): count files recursively in subfolders

- Commands in subfolders (tech/, product/, support/) now counted correctly
- Split count_files() into count_md_files() and count_script_files()
- Hooks counted as scripts (.sh/.js/.py/.ts), others as .md
- Excludes README.md from counts
- Bug: Was reporting 0 commands when 10 existed in subfolders
- Bump version to 2.9.6

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

claude-code-reference.yaml

@@ -3,7 +3,7 @@
 # Source: english-ultimate-claude-code-guide.md
 # Purpose: Condensed index for LLMs to quickly answer user questions about Claude Code
 
-version: "2.9.5"
+version: "2.9.6"
 updated: "2026-01"
 
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