[kevin9327]

Fixes #5097

Problem

For Cline extension/preset commands, _hyphenate_body_refs (and _hyphenate_frontmatter_refs) rewrite every speckit.<a>.<b> token. A file name such as speckit.git.commit.md matches as a reference, so .specify/extensions/git/commands/speckit.git.commit.md becomes .../speckit-git-commit-md (extension lost).

Fix

Both helpers now share one compiled pattern and a small replacer that leaves a match ending in .md unchanged. Command references such as /speckit.git.commit are still hyphenated.

Evidence

• Added test_cline_body_refs_keep_md_file_names and test_cline_frontmatter_refs_keep_md_file_names in tests/integrations/test_integration_cline.py.
• On main both fail; with this change both pass.
• pytest tests/integrations tests/test_extensions.py: 3632 passed, 8 skipped.

AI disclosure

Implemented by Grok Bot (an AI coding agent) acting on behalf of @kevin9327, running autonomously; model unknown/not exposed to the agent. Extent: code generation, tests, and this description. The commit carries an Assisted-by: trailer. I ran the tests above locally.

[Copilot]

🟡 Changes recommended

A moderate active issue remains because the .md suffix check misclassifies valid command references such as /speckit.foo.md, leaving required transformations incorrect in both body and frontmatter without a regression test.

1 open issue

• Handle .md command references separately from filenames · New

What changed in this PR

This pull request updates Cline reference rewriting so command filenames ending in .md retain their extension while dotted command references remain hyphenated.

Changes:

• Shares compiled matching and replacement logic for body and frontmatter references.
• Preserves .md-suffixed command filenames.
• Adds regression tests for body and frontmatter handling.

File	Summary
tests/​integrations/​test_integration_cline.py	Adds regression coverage for preserving .md command filenames in body and frontmatter references.
src/​specify_cli/​agents.py	Centralizes Cline reference rewriting, but the .md suffix check also leaves valid command references such as /speckit.foo.md unchanged; this requires a context-aware distinction.

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[mnriem]

Please address Copilot feedback

[Copilot]

🟡 Changes recommended

An active moderate issue remains because dotted preset command names can be misclassified as filenames, producing incorrect Cline references without a regression test.

1 open issue

• Handle dotted preset command names ending in md · New

1 resolved since last review

• Handle .md command references separately from filenames

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[mnriem]

Please address Copilot feedback

[Copilot]

🔵 Needs a closer look

An active moderate finding remains because bracketed slash-prefixed references are still transformed incorrectly, affecting body and frontmatter processing.

No open issues 🎉

1 previously missed issue

In code that hasn't changed since last review

Handle bracketed slash command references

src/​specify_cli/​agents.py:118

The slash-prefixed command rule still fails when the reference is immediately preceded by a Markdown [ (for example [/speckit.foo.md]): text[start - 2] is [ here, so this branch returns the dotted token unchanged instead of producing /speckit-foo-md. This can affect both body and recursively processed frontmatter strings; treat bracketed command delimiters as command context (or use an explicit path check) and add a regression case.

1 resolved since last review

• Handle dotted preset command names ending in md

_{Review effort: Lite (auto)}