[Bug]: Junie commands not recognized due to "dot" format

[lucabotti]

Bug Description

Current commands from specify init are not recognized by Junie CLI due to the "dot" format:

• speckit.analyze.md
• speckit.checklist.md
• ...
  are correctly created in the .junie/commands directory (under project) but are not available since junie does not recognize the format. Changing the command name (eg - "speckit-analyze.md") make it available in the CLI.

Steps to Reproduce

1. Create a directory "test" - mkdir test
2. cd test
3. specify init .
4. select Junie as agent integration
5. complete configuration (shell, py, ...)
6. start junie
7. no command available of the ones installed (/speckit does not find anything)

Expected Behavior

Commands should be available

Actual Behavior

No Speckit command available

Specify CLI Version

0.16.2

AI Agent

Junie

Operating System

Linux Fedora 44

Python Version

Python 3.14.0

Error Logs

No error logs

Additional Context

Renamed a command replacing the dot with a dash, and it works:

[github-actions]

Bug assessment — junie-dot-format-commands: Valid · severity medium

---

Bug Assessment: Junie commands not recognized due to dot format

• Slug: junie-dot-format-commands
• Created: 2026-08-12T16:01:08Z
• Source: issue [Bug]: Junie commands not recognized due to "dot" format #4067
• Verdict: valid
• Severity: medium

Report (summarized)

Reporter @lucabotti on Spec Kit v0.16.2 / Python 3.14.0 / Linux Fedora 44 finds that after running specify init with the Junie integration, all generated command files follow the dot-separated naming convention (e.g. speckit.analyze.md, speckit.checklist.md) in .junie/commands/. Junie CLI does not recognize this format; renaming a file to use dashes (e.g. speckit-analyze.md) immediately makes it discoverable. No error logs are produced — the commands are simply invisible in Junie's UI.

Symptom

Commands installed by Spec Kit into .junie/commands/ are named speckit.<name>.md, but the Junie CLI only recognizes commands with dash-separated filenames (e.g. speckit-<name>.md). As a result, none of the installed commands appear when the user opens Junie.

Reproduction

1. mkdir test && cd test
2. specify init .
3. Select Junie as the agent integration; complete remaining prompts.
4. Start Junie CLI.
5. Attempt to run /speckit — no commands are listed or found.

Suspected Code Paths

• src/specify_cli/integrations/junie/__init__.py — JunieIntegration does not override command_filename(), so it inherits the default from MarkdownIntegration.
• src/specify_cli/integrations/base.py:475–482 — MarkdownIntegration.command_filename() returns f"speckit.{template_name}.md" (dot-separated). This is the default for all markdown integrations; Junie requires a dash instead.

# base.py lines 475-482 (MarkdownIntegration)
def command_filename(self, template_name: str) -> str:
    """...Default: speckit.{template_name}.md..."""
    return f"speckit.{template_name}.md"

Root Cause Hypothesis

JunieIntegration inherits the dot-separated command_filename() from MarkdownIntegration without override, producing filenames that the Junie CLI does not recognize. Junie's file-discovery logic apparently requires a dash separator between speckit and the command name. Confidence: high — the reporter confirmed that manually renaming a file to use a dash resolves the issue, and the code shows no Junie-specific override exists.

Proposed Remediation

Preferred: Override command_filename() in JunieIntegration to return f"speckit-{template_name}.md":

def command_filename(self, template_name: str) -> str:
    return f"speckit-{template_name}.md"

This mirrors the same pattern already used by other integrations (e.g. Copilot's speckit.{name}.agent.md) and is the minimal, self-contained change. No other integration is affected.

Alternatives:

• A more general separator class attribute on MarkdownIntegration (e.g. separator = "." overridable to "-") would be cleaner for future integrations but adds abstraction complexity for what is currently a single-agent deviation.

Files likely to change:

• src/specify_cli/integrations/junie/__init__.py — add the command_filename() override.
• tests/integrations/test_integration_junie.py — update or add assertions checking that generated filenames use speckit-<name>.md.

Tests to add or update:

• Assert that JunieIntegration().command_filename("analyze") returns "speckit-analyze.md" (not "speckit.analyze.md").
• End-to-end install test: verify files created under .junie/commands/ all match the speckit-*.md pattern.

Risks & Considerations

• Existing installations: Users who already ran specify init with the Junie integration will have the old dot-named files in place. After the fix, a reinstall or uninstall+reinstall will be needed to get the correctly named files. The manifest system should handle cleanup of the old files on uninstall since their hashes are tracked.
• No API breakage: command_filename() is an internal method; the override is backward-compatible.
• build_command_invocation() in base.py (lines 325–328) constructs invocations like /speckit.<stem> — it would also need a review to ensure the slash-command format Junie expects (e.g. /speckit-analyze) is produced correctly, or documentation updated if Junie uses a different invocation convention.

Open Questions

• [NEEDS CLARIFICATION: Does Junie CLI use a specific invocation format (e.g. /speckit-analyze) that differs from what build_command_invocation() currently returns for Junie?]
• [NEEDS CLARIFICATION: Is the dash-separated format documented in Junie's official command authoring docs, or inferred solely from the reporter's workaround?]

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