Convert backtick-wrapped file paths to proper markdown links for
improved navigation and clickability in documentation viewers.

Changes:
- ~80+ file paths converted from `path/to/file.md` to
  [`path/to/file.md`](path/to/file.md) format
- 15 documentation files updated across AGENTS.md, README.md,
  TODO.md, CONTRIBUTING.md, and docs/ subdirectories
- All internal references now clickable in GitHub/GitLab