[Bug]: Cline extension and preset commands have speckit.*.md file names rewritten to speckit-*-md #5097

Bug Description

When an extension or preset command is registered for Cline (src/specify_cli/agents.py:718, 831-833), the command body goes through CommandRegistrar._hyphenate_body_refs (agents.py:114-120). This replaces every dot in any speckit.<a>.<b>... token with a hyphen, so that command references match Cline's hyphenated file names. The regex also matches file names, so a path such as speckit.git.commit.md becomes speckit-git-commit-md, which names no file. The frontmatter goes through the same rewrite in _hyphenate_frontmatter_refs (agents.py:96-111).

The expectation here is inferred rather than documented. The bundled extensions name their command files speckit.<ext>.<cmd>.md (extensions/git/extension.yml:21-33). The extension development guide refers to files by those names (extensions/EXTENSION-DEVELOPMENT-GUIDE.md:306-308). The method's docstring describes its purpose as hyphenating "dotted speckit references". I could not find a doc or test that says file names should be rewritten too.

Steps to Reproduce

From a fresh clone, after uv sync, save the script below and run uv run python -I repro.py from the repository root.

from specify_cli.agents import CommandRegistrar

body = "Edit `.specify/extensions/git/commands/speckit.git.commit.md`, then run /speckit.git.commit."
print("in :", body)
print("out:", CommandRegistrar._hyphenate_body_refs(body))

Expected Behavior

The command reference /speckit.git.commit should become /speckit-git-commit, and the file name speckit.git.commit.md should be left alone (or at least keep its .md extension). This is inferred from the file naming in extensions/git/extension.yml:21-33 and extensions/EXTENSION-DEVELOPMENT-GUIDE.md:306-308, as described above.

Actual Behavior

in : Edit `.specify/extensions/git/commands/speckit.git.commit.md`, then run /speckit.git.commit.
out: Edit `.specify/extensions/git/commands/speckit-git-commit-md`, then run /speckit-git-commit.

Specify CLI Version

1.2.4.dev0 (main at 27d14e2)

AI Agent

Cline

Operating System

Linux 6.18 (Ubuntu container)

Python Version

Python 3.12.3

Additional Context

This only affects Cline, and only command bodies (from extensions or presets) that mention spec-kit command file names.

Also reproduced on macOS (Darwin 25.6, arm64) with Python 3.14.4 and uv run python -I repro.py against 27d14e2; the output matches the above.

AI Disclosure

Found and reproduced with Claude Code (model: Claude Opus 4.8), run autonomously under human supervision. The human reporter re-ran every reproduction above before filing.