From b5757e657f1594f4232afe7cceb48140647ae73b Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Fri, 24 Apr 2026 08:35:18 -0500
Subject: [PATCH 1/4] fix: resolve command references per integration type (dot
 vs hyphen)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Replace hardcoded /speckit.<cmd> references in templates with
__SPECKIT_COMMAND_<NAME>__ placeholders that are resolved at
setup time based on the integration type:

- Markdown/TOML/YAML agents: separator='.' → /speckit.plan
- Skills agents: separator='-' → /speckit-plan

Changes:
- Add resolve_command_refs() static method to IntegrationBase
- Add invoke_separator class attribute (.  for base, - for skills)
- Wire into process_template() as step 8
- Update _install_shared_infra() to process page templates
- Replace /speckit.* in 5 command templates and 3 page templates
- Add unit tests for resolve_command_refs (positive + negative)
- Add integration tests verifying on-disk content for all agents
- Add end-to-end CLI tests for Claude (skills) and Copilot (markdown)

Fixes #2347
---
 src/specify_cli/__init__.py                   |  20 +++-
 src/specify_cli/integrations/base.py          |  29 +++++
 templates/checklist-template.md               |   4 +-
 templates/commands/analyze.md                 |   8 +-
 templates/commands/checklist.md               |   2 +-
 templates/commands/clarify.md                 |   8 +-
 templates/commands/implement.md               |   2 +-
 templates/commands/specify.md                 |  10 +-
 templates/plan-template.md                    |  14 +--
 templates/tasks-template.md                   |   2 +-
 tests/integrations/test_base.py               |  80 ++++++++++++++
 tests/integrations/test_cli.py                | 101 ++++++++++++++++++
 .../test_integration_base_markdown.py         |   1 +
 .../test_integration_base_skills.py           |  16 +++
 .../test_integration_base_toml.py             |   1 +
 .../test_integration_base_yaml.py             |   1 +
 tests/integrations/test_integration_claude.py |   2 +
 .../integrations/test_integration_copilot.py  |   1 +
 tests/integrations/test_integration_forge.py  |   1 +
 .../integrations/test_integration_generic.py  |   1 +
 20 files changed, 274 insertions(+), 30 deletions(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 77611128b5..8d593abefb 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -723,6 +723,7 @@ def _install_shared_infra(
     script_type: str,
     tracker: StepTracker | None = None,
     force: bool = False,
+    invoke_separator: str = ".",
 ) -> bool:
     """Install shared infrastructure files into *project_path*.
 
@@ -730,12 +731,17 @@ def _install_shared_infra(
     bundled core_pack or source checkout.  Tracks all installed files
     in ``speckit.manifest.json``.
 
+    Page templates are processed to resolve ``__SPECKIT_COMMAND_<NAME>__``
+    placeholders using *invoke_separator* (``"."`` for markdown agents,
+    ``"-"`` for skills agents).
+
     When *force* is ``True``, existing files are overwritten with the
     latest bundled versions.  When ``False`` (default), only missing
     files are added and existing ones are skipped.
 
     Returns ``True`` on success.
     """
+    from .integrations.base import IntegrationBase
     from .integrations.manifest import IntegrationManifest
 
     core = _locate_core_pack()
@@ -786,7 +792,11 @@ def _install_shared_infra(
                 if dst.exists() and not force:
                     skipped_files.append(str(dst.relative_to(project_path)))
                 else:
-                    shutil.copy2(f, dst)
+                    content = f.read_text(encoding="utf-8")
+                    content = IntegrationBase.resolve_command_refs(
+                        content, invoke_separator
+                    )
+                    dst.write_text(content, encoding="utf-8")
                     rel = dst.relative_to(project_path).as_posix()
                     manifest.record_existing(rel)
 
@@ -1295,7 +1305,7 @@ def init(
 
             # Install shared infrastructure (scripts, templates)
             tracker.start("shared-infra")
-            _install_shared_infra(project_path, selected_script, tracker=tracker, force=force)
+            _install_shared_infra(project_path, selected_script, tracker=tracker, force=force, invoke_separator=resolved_integration.invoke_separator)
             tracker.complete("shared-infra", f"scripts ({selected_script}) + templates")
 
             ensure_constitution_from_template(project_path, tracker=tracker)
@@ -2074,7 +2084,7 @@ def integration_install(
 
     # Ensure shared infrastructure is present (safe to run unconditionally;
     # _install_shared_infra merges missing files without overwriting).
-    _install_shared_infra(project_root, selected_script)
+    _install_shared_infra(project_root, selected_script, invoke_separator=integration.invoke_separator)
     if os.name != "nt":
         ensure_executable_scripts(project_root)
 
@@ -2358,7 +2368,7 @@ def integration_switch(
 
     # Ensure shared infrastructure is present (safe to run unconditionally;
     # _install_shared_infra merges missing files without overwriting).
-    _install_shared_infra(project_root, selected_script)
+    _install_shared_infra(project_root, selected_script, invoke_separator=target_integration.invoke_separator)
     if os.name != "nt":
         ensure_executable_scripts(project_root)
 
@@ -2466,7 +2476,7 @@ def integration_upgrade(
     selected_script = _resolve_script_type(project_root, script)
 
     # Ensure shared infrastructure is up to date; --force overwrites existing files.
-    _install_shared_infra(project_root, selected_script, force=force)
+    _install_shared_infra(project_root, selected_script, force=force, invoke_separator=integration.invoke_separator)
     if os.name != "nt":
         ensure_executable_scripts(project_root)
 
diff --git a/src/specify_cli/integrations/base.py b/src/specify_cli/integrations/base.py
index a3d8a42aa2..16deb9647a 100644
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -84,6 +84,9 @@ class IntegrationBase(ABC):
     context_file: str | None = None
     """Relative path to the agent context file (e.g. ``CLAUDE.md``)."""
 
+    invoke_separator: str = "."
+    """Separator used in slash-command invocations (``"."`` → ``/speckit.plan``)."""
+
     # -- Markers for managed context section ------------------------------
 
     CONTEXT_MARKER_START = "<!-- SPECKIT START -->"
@@ -597,6 +600,24 @@ def remove_context_section(self, project_root: Path) -> bool:
 
         return True
 
+    @staticmethod
+    def resolve_command_refs(content: str, separator: str = ".") -> str:
+        """Replace ``__SPECKIT_COMMAND_<NAME>__`` placeholders with invocations.
+
+        Each placeholder encodes a command name in upper-case with
+        underscores (e.g. ``__SPECKIT_COMMAND_PLAN__``,
+        ``__SPECKIT_COMMAND_GIT_COMMIT__``).  The replacement uses
+        *separator* to join the segments:
+
+        * ``separator="."`` → ``/speckit.plan``, ``/speckit.git.commit``
+        * ``separator="-"`` → ``/speckit-plan``, ``/speckit-git-commit``
+        """
+        return re.sub(
+            r"__SPECKIT_COMMAND_([A-Z][A-Z0-9_]*)__",
+            lambda m: "/speckit" + separator + m.group(1).lower().replace("_", separator),
+            content,
+        )
+
     @staticmethod
     def process_template(
         content: str,
@@ -604,6 +625,7 @@ def process_template(
         script_type: str,
         arg_placeholder: str = "$ARGUMENTS",
         context_file: str = "",
+        invoke_separator: str = ".",
     ) -> str:
         """Process a raw command template into agent-ready content.
 
@@ -615,6 +637,7 @@ def process_template(
         5. Replace ``__AGENT__`` with *agent_name*
         6. Replace ``__CONTEXT_FILE__`` with *context_file*
         7. Rewrite paths: ``scripts/`` → ``.specify/scripts/`` etc.
+        8. Replace ``__SPECKIT_COMMAND_<NAME>__`` with invocation strings
         """
         # 1. Extract script command from frontmatter
         script_command = ""
@@ -684,6 +707,9 @@ def process_template(
 
         content = CommandRegistrar.rewrite_project_relative_paths(content)
 
+        # 8. Replace __SPECKIT_COMMAND_<NAME>__ with invocation strings
+        content = IntegrationBase.resolve_command_refs(content, invoke_separator)
+
         return content
 
     def setup(
@@ -1274,6 +1300,8 @@ class SkillsIntegration(IntegrationBase):
     ``speckit-<name>/SKILL.md`` file with skills-oriented frontmatter.
     """
 
+    invoke_separator = "-"
+
     def build_exec_args(
         self,
         prompt: str,
@@ -1395,6 +1423,7 @@ def setup(
             processed_body = self.process_template(
                 raw, self.key, script_type, arg_placeholder,
                 context_file=self.context_file or "",
+                invoke_separator=self.invoke_separator,
             )
             # Strip the processed frontmatter — we rebuild it for skills.
             # Preserve leading whitespace in the body to match release ZIP
diff --git a/templates/checklist-template.md b/templates/checklist-template.md
index 806657da09..9752c130ec 100644
--- a/templates/checklist-template.md
+++ b/templates/checklist-template.md
@@ -4,13 +4,13 @@
 **Created**: [DATE]
 **Feature**: [Link to spec.md or relevant documentation]
 
-**Note**: This checklist is generated by the `/speckit.checklist` command based on feature context and requirements.
+**Note**: This checklist is generated by the `__SPECKIT_COMMAND_CHECKLIST__` command based on feature context and requirements.
 
 <!-- 
   ============================================================================
   IMPORTANT: The checklist items below are SAMPLE ITEMS for illustration only.
   
-  The /speckit.checklist command MUST replace these with actual items based on:
+  The __SPECKIT_COMMAND_CHECKLIST__ command MUST replace these with actual items based on:
   - User's specific checklist request
   - Feature requirements from spec.md
   - Technical context from plan.md
diff --git a/templates/commands/analyze.md b/templates/commands/analyze.md
index 43e6d225b1..5b521cf2a4 100644
--- a/templates/commands/analyze.md
+++ b/templates/commands/analyze.md
@@ -49,13 +49,13 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 ## Goal
 
-Identify inconsistencies, duplications, ambiguities, and underspecified items across the three core artifacts (`spec.md`, `plan.md`, `tasks.md`) before implementation. This command MUST run only after `/speckit.tasks` has successfully produced a complete `tasks.md`.
+Identify inconsistencies, duplications, ambiguities, and underspecified items across the three core artifacts (`spec.md`, `plan.md`, `tasks.md`) before implementation. This command MUST run only after `__SPECKIT_COMMAND_TASKS__` has successfully produced a complete `tasks.md`.
 
 ## Operating Constraints
 
 **STRICTLY READ-ONLY**: Do **not** modify any files. Output a structured analysis report. Offer an optional remediation plan (user must explicitly approve before any follow-up editing commands would be invoked manually).
 
-**Constitution Authority**: The project constitution (`/memory/constitution.md`) is **non-negotiable** within this analysis scope. Constitution conflicts are automatically CRITICAL and require adjustment of the spec, plan, or tasks—not dilution, reinterpretation, or silent ignoring of the principle. If a principle itself needs to change, that must occur in a separate, explicit constitution update outside `/speckit.analyze`.
+**Constitution Authority**: The project constitution (`/memory/constitution.md`) is **non-negotiable** within this analysis scope. Constitution conflicts are automatically CRITICAL and require adjustment of the spec, plan, or tasks—not dilution, reinterpretation, or silent ignoring of the principle. If a principle itself needs to change, that must occur in a separate, explicit constitution update outside `__SPECKIT_COMMAND_ANALYZE__`.
 
 ## Execution Steps
 
@@ -191,9 +191,9 @@ Output a Markdown report (no file writes) with the following structure:
 
 At end of report, output a concise Next Actions block:
 
-- If CRITICAL issues exist: Recommend resolving before `/speckit.implement`
+- If CRITICAL issues exist: Recommend resolving before `__SPECKIT_COMMAND_IMPLEMENT__`
 - If only LOW/MEDIUM: User may proceed, but provide improvement suggestions
-- Provide explicit command suggestions: e.g., "Run /speckit.specify with refinement", "Run /speckit.plan to adjust architecture", "Manually edit tasks.md to add coverage for 'performance-metrics'"
+- Provide explicit command suggestions: e.g., "Run __SPECKIT_COMMAND_SPECIFY__ with refinement", "Run __SPECKIT_COMMAND_PLAN__ to adjust architecture", "Manually edit tasks.md to add coverage for 'performance-metrics'"
 
 ### 8. Offer Remediation
 
diff --git a/templates/commands/checklist.md b/templates/commands/checklist.md
index 533046566b..3e400d86e3 100644
--- a/templates/commands/checklist.md
+++ b/templates/commands/checklist.md
@@ -249,7 +249,7 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Actor/timing
    - Any explicit user-specified must-have items incorporated
 
-**Important**: Each `/speckit.checklist` command invocation uses a short, descriptive checklist filename and either creates a new file or appends to an existing one. This allows:
+**Important**: Each `__SPECKIT_COMMAND_CHECKLIST__` command invocation uses a short, descriptive checklist filename and either creates a new file or appends to an existing one. This allows:
 
 - Multiple checklists of different types (e.g., `ux.md`, `test.md`, `security.md`)
 - Simple, memorable filenames that indicate checklist purpose
diff --git a/templates/commands/clarify.md b/templates/commands/clarify.md
index d6d6bbe910..57cd01def1 100644
--- a/templates/commands/clarify.md
+++ b/templates/commands/clarify.md
@@ -55,7 +55,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 Goal: Detect and reduce ambiguity or missing decision points in the active feature specification and record the clarifications directly in the spec file.
 
-Note: This clarification workflow is expected to run (and be completed) BEFORE invoking `/speckit.plan`. If the user explicitly states they are skipping clarification (e.g., exploratory spike), you may proceed, but must warn that downstream rework risk increases.
+Note: This clarification workflow is expected to run (and be completed) BEFORE invoking `__SPECKIT_COMMAND_PLAN__`. If the user explicitly states they are skipping clarification (e.g., exploratory spike), you may proceed, but must warn that downstream rework risk increases.
 
 Execution steps:
 
@@ -63,7 +63,7 @@ Execution steps:
    - `FEATURE_DIR`
    - `FEATURE_SPEC`
    - (Optionally capture `IMPL_PLAN`, `TASKS` for future chained flows.)
-   - If JSON parsing fails, abort and instruct user to re-run `/speckit.specify` or verify feature branch environment.
+   - If JSON parsing fails, abort and instruct user to re-run `__SPECKIT_COMMAND_SPECIFY__` or verify feature branch environment.
    - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
 
 2. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).
@@ -202,13 +202,13 @@ Execution steps:
    - Path to updated spec.
    - Sections touched (list names).
    - Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
-   - If any Outstanding or Deferred remain, recommend whether to proceed to `/speckit.plan` or run `/speckit.clarify` again later post-plan.
+   - If any Outstanding or Deferred remain, recommend whether to proceed to `__SPECKIT_COMMAND_PLAN__` or run `__SPECKIT_COMMAND_CLARIFY__` again later post-plan.
    - Suggested next command.
 
 Behavior rules:
 
 - If no meaningful ambiguities found (or all potential questions would be low-impact), respond: "No critical ambiguities detected worth formal clarification." and suggest proceeding.
-- If spec file missing, instruct user to run `/speckit.specify` first (do not create a new spec here).
+- If spec file missing, instruct user to run `__SPECKIT_COMMAND_SPECIFY__` first (do not create a new spec here).
 - Never exceed 5 total asked questions (clarification retries for a single question do not count as new questions).
 - Avoid speculative tech stack questions unless the absence blocks functional clarity.
 - Respect user early termination signals ("stop", "done", "proceed").
diff --git a/templates/commands/implement.md b/templates/commands/implement.md
index 9a91d2dc4b..7ba5ba8e0c 100644
--- a/templates/commands/implement.md
+++ b/templates/commands/implement.md
@@ -169,7 +169,7 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Confirm the implementation follows the technical plan
    - Report final status with summary of completed work
 
-Note: This command assumes a complete task breakdown exists in tasks.md. If tasks are incomplete or missing, suggest running `/speckit.tasks` first to regenerate the task list.
+Note: This command assumes a complete task breakdown exists in tasks.md. If tasks are incomplete or missing, suggest running `__SPECKIT_COMMAND_TASKS__` first to regenerate the task list.
 
 10. **Check for extension hooks**: After completion validation, check if `.specify/extensions.yml` exists in the project root.
     - If it exists, read it and look for entries under the `hooks.after_implement` key
diff --git a/templates/commands/specify.md b/templates/commands/specify.md
index 15c75ec396..1f3f5c4465 100644
--- a/templates/commands/specify.md
+++ b/templates/commands/specify.md
@@ -54,7 +54,7 @@ You **MUST** consider the user input before proceeding (if not empty).
 
 ## Outline
 
-The text the user typed after `/speckit.specify` in the triggering message **is** the feature description. Assume you always have it available in this conversation even if `{ARGS}` appears literally below. Do not ask the user to repeat it unless they provided an empty command.
+The text the user typed after `__SPECKIT_COMMAND_SPECIFY__` in the triggering message **is** the feature description. Assume you always have it available in this conversation even if `{ARGS}` appears literally below. Do not ask the user to repeat it unless they provided an empty command.
 
 Given that feature description, do this:
 
@@ -100,10 +100,10 @@ Given that feature description, do this:
      }
      ```
      Write the actual resolved directory path value (for example, `specs/003-user-auth`), not the literal string `SPECIFY_FEATURE_DIRECTORY`.
-     This allows downstream commands (`/speckit.plan`, `/speckit.tasks`, etc.) to locate the feature directory without relying on git branch name conventions.
+     This allows downstream commands (`__SPECKIT_COMMAND_PLAN__`, `__SPECKIT_COMMAND_TASKS__`, etc.) to locate the feature directory without relying on git branch name conventions.
 
    **IMPORTANT**:
-   - You must only create one feature per `/speckit.specify` invocation
+   - You must only create one feature per `__SPECKIT_COMMAND_SPECIFY__` invocation
    - The spec directory name and the git branch name are independent — they may be the same but that is the user's choice
    - The spec directory and file are always created by this command, never by the hook
 
@@ -174,7 +174,7 @@ Given that feature description, do this:
       
       ## Notes
       
-      - Items marked incomplete require spec updates before `/speckit.clarify` or `/speckit.plan`
+      - Items marked incomplete require spec updates before `__SPECKIT_COMMAND_CLARIFY__` or `__SPECKIT_COMMAND_PLAN__`
       ```
 
    b. **Run Validation Check**: Review the spec against each checklist item:
@@ -232,7 +232,7 @@ Given that feature description, do this:
    - `SPECIFY_FEATURE_DIRECTORY` — the feature directory path
    - `SPEC_FILE` — the spec file path
    - Checklist results summary
-   - Readiness for the next phase (`/speckit.clarify` or `/speckit.plan`)
+   - Readiness for the next phase (`__SPECKIT_COMMAND_CLARIFY__` or `__SPECKIT_COMMAND_PLAN__`)
 
 9. **Check for extension hooks**: After reporting completion, check if `.specify/extensions.yml` exists in the project root.
    - If it exists, read it and look for entries under the `hooks.after_specify` key
diff --git a/templates/plan-template.md b/templates/plan-template.md
index 5a2fafebe3..ee57c35656 100644
--- a/templates/plan-template.md
+++ b/templates/plan-template.md
@@ -3,7 +3,7 @@
 **Branch**: `[###-feature-name]` | **Date**: [DATE] | **Spec**: [link]
 **Input**: Feature specification from `/specs/[###-feature-name]/spec.md`
 
-**Note**: This template is filled in by the `/speckit.plan` command. See `.specify/templates/plan-template.md` for the execution workflow.
+**Note**: This template is filled in by the `__SPECKIT_COMMAND_PLAN__` command. See `.specify/templates/plan-template.md` for the execution workflow.
 
 ## Summary
 
@@ -39,12 +39,12 @@
 
 ```text
 specs/[###-feature]/
-├── plan.md              # This file (/speckit.plan command output)
-├── research.md          # Phase 0 output (/speckit.plan command)
-├── data-model.md        # Phase 1 output (/speckit.plan command)
-├── quickstart.md        # Phase 1 output (/speckit.plan command)
-├── contracts/           # Phase 1 output (/speckit.plan command)
-└── tasks.md             # Phase 2 output (/speckit.tasks command - NOT created by /speckit.plan)
+├── plan.md              # This file (__SPECKIT_COMMAND_PLAN__ command output)
+├── research.md          # Phase 0 output (__SPECKIT_COMMAND_PLAN__ command)
+├── data-model.md        # Phase 1 output (__SPECKIT_COMMAND_PLAN__ command)
+├── quickstart.md        # Phase 1 output (__SPECKIT_COMMAND_PLAN__ command)
+├── contracts/           # Phase 1 output (__SPECKIT_COMMAND_PLAN__ command)
+└── tasks.md             # Phase 2 output (__SPECKIT_COMMAND_TASKS__ command - NOT created by __SPECKIT_COMMAND_PLAN__)
 ```
 
 ### Source Code (repository root)
diff --git a/templates/tasks-template.md b/templates/tasks-template.md
index 60f9be455d..cc649380b9 100644
--- a/templates/tasks-template.md
+++ b/templates/tasks-template.md
@@ -29,7 +29,7 @@ description: "Task list template for feature implementation"
   ============================================================================
   IMPORTANT: The tasks below are SAMPLE TASKS for illustration purposes only.
   
-  The /speckit.tasks command MUST replace these with actual tasks based on:
+  The __SPECKIT_COMMAND_TASKS__ command MUST replace these with actual tasks based on:
   - User stories from spec.md (with their priorities P1, P2, P3...)
   - Feature requirements from plan.md
   - Entities from data-model.md
diff --git a/tests/integrations/test_base.py b/tests/integrations/test_base.py
index 03b5eb3068..13218e19b2 100644
--- a/tests/integrations/test_base.py
+++ b/tests/integrations/test_base.py
@@ -6,6 +6,7 @@
     IntegrationBase,
     IntegrationOption,
     MarkdownIntegration,
+    SkillsIntegration,
 )
 from specify_cli.integrations.manifest import IntegrationManifest
 from .conftest import StubIntegration
@@ -167,3 +168,82 @@ def test_setup_copies_shared_templates(self, tmp_path):
             assert f.parent.name == "commands"
             assert f.name.startswith("speckit.")
             assert f.name.endswith(".md")
+
+
+class TestResolveCommandRefs:
+    """Tests for __SPECKIT_COMMAND_<NAME>__ placeholder resolution."""
+
+    def test_dot_separator_core_command(self):
+        text = "Run `__SPECKIT_COMMAND_PLAN__` to plan."
+        result = IntegrationBase.resolve_command_refs(text, ".")
+        assert result == "Run `/speckit.plan` to plan."
+
+    def test_hyphen_separator_core_command(self):
+        text = "Run `__SPECKIT_COMMAND_PLAN__` to plan."
+        result = IntegrationBase.resolve_command_refs(text, "-")
+        assert result == "Run `/speckit-plan` to plan."
+
+    def test_multiple_placeholders(self):
+        text = "__SPECKIT_COMMAND_SPECIFY__ then __SPECKIT_COMMAND_PLAN__ then __SPECKIT_COMMAND_TASKS__"
+        result = IntegrationBase.resolve_command_refs(text, ".")
+        assert result == "/speckit.specify then /speckit.plan then /speckit.tasks"
+
+    def test_extension_command_dot(self):
+        text = "Run __SPECKIT_COMMAND_GIT_COMMIT__ to commit."
+        result = IntegrationBase.resolve_command_refs(text, ".")
+        assert result == "Run /speckit.git.commit to commit."
+
+    def test_extension_command_hyphen(self):
+        text = "Run __SPECKIT_COMMAND_GIT_COMMIT__ to commit."
+        result = IntegrationBase.resolve_command_refs(text, "-")
+        assert result == "Run /speckit-git-commit to commit."
+
+    def test_no_placeholders_unchanged(self):
+        text = "No placeholders here."
+        assert IntegrationBase.resolve_command_refs(text, ".") == text
+
+    def test_default_separator_is_dot(self):
+        text = "__SPECKIT_COMMAND_PLAN__"
+        assert IntegrationBase.resolve_command_refs(text) == "/speckit.plan"
+
+    def test_invoke_separator_class_attribute(self):
+        assert IntegrationBase.invoke_separator == "."
+        assert SkillsIntegration.invoke_separator == "-"
+
+    def test_process_template_resolves_placeholders(self):
+        content = "---\ndescription: test\n---\nRun __SPECKIT_COMMAND_PLAN__ now."
+        result = IntegrationBase.process_template(
+            content, "test-agent", "sh", invoke_separator="."
+        )
+        assert "/speckit.plan" in result
+        assert "__SPECKIT_COMMAND_" not in result
+
+    def test_process_template_skills_separator(self):
+        content = "---\ndescription: test\n---\nRun __SPECKIT_COMMAND_PLAN__ now."
+        result = IntegrationBase.process_template(
+            content, "test-agent", "sh", invoke_separator="-"
+        )
+        assert "/speckit-plan" in result
+        assert "__SPECKIT_COMMAND_" not in result
+
+    def test_unclosed_placeholder_unchanged(self):
+        text = "Run __SPECKIT_COMMAND_PLAN to plan."
+        assert IntegrationBase.resolve_command_refs(text, ".") == text
+
+    def test_empty_name_not_matched(self):
+        text = "Run __SPECKIT_COMMAND___ to plan."
+        assert IntegrationBase.resolve_command_refs(text, ".") == text
+
+    def test_lowercase_placeholder_not_matched(self):
+        text = "Run __SPECKIT_COMMAND_plan__ to plan."
+        assert IntegrationBase.resolve_command_refs(text, ".") == text
+
+    def test_placeholder_adjacent_to_text(self):
+        text = "foo__SPECKIT_COMMAND_PLAN__bar"
+        result = IntegrationBase.resolve_command_refs(text, ".")
+        assert result == "foo/speckit.planbar"
+
+    def test_placeholder_with_digits(self):
+        text = "__SPECKIT_COMMAND_V2_PLAN__"
+        result = IntegrationBase.resolve_command_refs(text, ".")
+        assert result == "/speckit.v2.plan"
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index 9672ab76bf..0df43ac1e1 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -471,3 +471,104 @@ def test_git_extension_commands_registered(self, tmp_path):
         assert claude_skills.exists(), "Claude skills directory was not created"
         git_skills = [f for f in claude_skills.iterdir() if f.name.startswith("speckit-git-")]
         assert len(git_skills) > 0, "no git extension commands registered"
+
+
+class TestSharedInfraCommandRefs:
+    """Verify _install_shared_infra resolves __SPECKIT_COMMAND_*__ in page templates."""
+
+    def test_dot_separator_in_page_templates(self, tmp_path):
+        """Markdown agents get /speckit.<name> in page templates."""
+        from specify_cli import _install_shared_infra
+
+        project = tmp_path / "dot-test"
+        project.mkdir()
+        (project / ".specify").mkdir()
+
+        _install_shared_infra(project, "sh", invoke_separator=".")
+
+        plan = project / ".specify" / "templates" / "plan-template.md"
+        assert plan.exists()
+        content = plan.read_text(encoding="utf-8")
+        assert "__SPECKIT_COMMAND_" not in content, "unresolved placeholder in plan-template.md"
+        assert "/speckit.plan" in content
+
+        checklist = project / ".specify" / "templates" / "checklist-template.md"
+        content = checklist.read_text(encoding="utf-8")
+        assert "__SPECKIT_COMMAND_" not in content
+        assert "/speckit.checklist" in content
+
+    def test_hyphen_separator_in_page_templates(self, tmp_path):
+        """Skills agents get /speckit-<name> in page templates."""
+        from specify_cli import _install_shared_infra
+
+        project = tmp_path / "hyphen-test"
+        project.mkdir()
+        (project / ".specify").mkdir()
+
+        _install_shared_infra(project, "sh", invoke_separator="-")
+
+        plan = project / ".specify" / "templates" / "plan-template.md"
+        assert plan.exists()
+        content = plan.read_text(encoding="utf-8")
+        assert "__SPECKIT_COMMAND_" not in content, "unresolved placeholder in plan-template.md"
+        assert "/speckit-plan" in content
+        assert "/speckit.plan" not in content, "dot-notation leaked into skills page template"
+
+        tasks = project / ".specify" / "templates" / "tasks-template.md"
+        content = tasks.read_text(encoding="utf-8")
+        assert "__SPECKIT_COMMAND_" not in content
+        assert "/speckit-tasks" in content
+
+    def test_full_init_claude_resolves_page_templates(self, tmp_path):
+        """Full CLI init with Claude (skills agent) produces hyphen refs in page templates."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "init-claude"
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(app, [
+                "init", str(project),
+                "--integration", "claude",
+                "--script", "sh",
+                "--no-git",
+                "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, f"init failed: {result.output}"
+
+        plan = project / ".specify" / "templates" / "plan-template.md"
+        content = plan.read_text(encoding="utf-8")
+        assert "/speckit-plan" in content, "Claude (skills) should use /speckit-plan"
+        assert "__SPECKIT_COMMAND_" not in content
+
+    def test_full_init_copilot_resolves_page_templates(self, tmp_path):
+        """Full CLI init with Copilot (markdown agent) produces dot refs in page templates."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "init-copilot"
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(app, [
+                "init", str(project),
+                "--integration", "copilot",
+                "--script", "sh",
+                "--no-git",
+                "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, f"init failed: {result.output}"
+
+        plan = project / ".specify" / "templates" / "plan-template.md"
+        content = plan.read_text(encoding="utf-8")
+        assert "/speckit.plan" in content, "Copilot (markdown) should use /speckit.plan"
+        assert "__SPECKIT_COMMAND_" not in content
diff --git a/tests/integrations/test_integration_base_markdown.py b/tests/integrations/test_integration_base_markdown.py
index f22bb298b4..82d7b8cfb3 100644
--- a/tests/integrations/test_integration_base_markdown.py
+++ b/tests/integrations/test_integration_base_markdown.py
@@ -98,6 +98,7 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{f.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{f.name} has unprocessed __SPECKIT_COMMAND_*__"
             assert "\nscripts:\n" not in content, f"{f.name} has unstripped scripts: block"
 
     def test_plan_references_correct_context_file(self, tmp_path):
diff --git a/tests/integrations/test_integration_base_skills.py b/tests/integrations/test_integration_base_skills.py
index c8c152a84b..98a65fcff4 100644
--- a/tests/integrations/test_integration_base_skills.py
+++ b/tests/integrations/test_integration_base_skills.py
@@ -159,6 +159,22 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{f.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{f.name} has unprocessed __SPECKIT_COMMAND_*__"
+
+    def test_command_refs_use_hyphen_separator(self, tmp_path):
+        """Skills agents must resolve command refs with hyphen separator."""
+        i = get_integration(self.KEY)
+        m = IntegrationManifest(self.KEY, tmp_path)
+        created = i.setup(tmp_path, m)
+        skill_files = [f for f in created if "scripts" not in f.parts]
+        assert len(skill_files) > 0
+        for f in skill_files:
+            content = f.read_text(encoding="utf-8")
+            # Skills agents must use /speckit-<name>, not /speckit.<name>
+            assert "/speckit." not in content, (
+                f"{f.name} contains dot-notation /speckit. reference; "
+                f"skills agents must use /speckit-<name>"
+            )
 
     def test_skill_body_has_content(self, tmp_path):
         """Each SKILL.md body should contain template content after the frontmatter."""
diff --git a/tests/integrations/test_integration_base_toml.py b/tests/integrations/test_integration_base_toml.py
index ca66b2123a..78273b560e 100644
--- a/tests/integrations/test_integration_base_toml.py
+++ b/tests/integrations/test_integration_base_toml.py
@@ -106,6 +106,7 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{f.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{f.name} has unprocessed __SPECKIT_COMMAND_*__"
 
     def test_toml_has_description(self, tmp_path):
         """Every TOML command file should have a description key."""
diff --git a/tests/integrations/test_integration_base_yaml.py b/tests/integrations/test_integration_base_yaml.py
index 08f088576c..e1dee3bad7 100644
--- a/tests/integrations/test_integration_base_yaml.py
+++ b/tests/integrations/test_integration_base_yaml.py
@@ -105,6 +105,7 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{f.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{f.name} has unprocessed __SPECKIT_COMMAND_*__"
 
     def test_yaml_has_title(self, tmp_path):
         """Every YAML recipe should have a title field."""
diff --git a/tests/integrations/test_integration_claude.py b/tests/integrations/test_integration_claude.py
index 72e73bb02b..b3236a66b7 100644
--- a/tests/integrations/test_integration_claude.py
+++ b/tests/integrations/test_integration_claude.py
@@ -55,6 +55,8 @@ def test_setup_creates_skill_files(self, tmp_path):
         assert "{SCRIPT}" not in content
         assert "{ARGS}" not in content
         assert "__AGENT__" not in content
+        assert "__SPECKIT_COMMAND_" not in content, "unprocessed __SPECKIT_COMMAND_*__"
+        assert "/speckit." not in content, "skills agent must use /speckit-<name> not /speckit.<name>"
 
         parts = content.split("---", 2)
         parsed = yaml.safe_load(parts[1])
diff --git a/tests/integrations/test_integration_copilot.py b/tests/integrations/test_integration_copilot.py
index 462f6d120a..688fb9dd8d 100644
--- a/tests/integrations/test_integration_copilot.py
+++ b/tests/integrations/test_integration_copilot.py
@@ -144,6 +144,7 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{agent_file.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{agent_file.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{agent_file.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{agent_file.name} has unprocessed __SPECKIT_COMMAND_*__"
             assert "\nscripts:\n" not in content
 
     def test_plan_references_correct_context_file(self, tmp_path):
diff --git a/tests/integrations/test_integration_forge.py b/tests/integrations/test_integration_forge.py
index 613ede91c0..8cd8b17c95 100644
--- a/tests/integrations/test_integration_forge.py
+++ b/tests/integrations/test_integration_forge.py
@@ -152,6 +152,7 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{cmd_file.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{cmd_file.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{cmd_file.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{cmd_file.name} has unprocessed __SPECKIT_COMMAND_*__"
             # Check Forge-specific: $ARGUMENTS should be replaced with {{parameters}}
             assert "$ARGUMENTS" not in content, f"{cmd_file.name} has unprocessed $ARGUMENTS"
             # Frontmatter sections should be stripped
diff --git a/tests/integrations/test_integration_generic.py b/tests/integrations/test_integration_generic.py
index 8ca32078b5..f0272afa8d 100644
--- a/tests/integrations/test_integration_generic.py
+++ b/tests/integrations/test_integration_generic.py
@@ -101,6 +101,7 @@ def test_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{f.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{f.name} has unprocessed __SPECKIT_COMMAND_*__"
 
     def test_all_files_tracked_in_manifest(self, tmp_path):
         i = get_integration("generic")

From 109c247e570c73c096d082dcac49c7c574926c6d Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Fri, 24 Apr 2026 09:35:15 -0500
Subject: [PATCH 2/4] review: use effective_invoke_separator() for Copilot
 skills mode
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Address PR review feedback: instead of bleeding _skills_mode
knowledge into the CLI layer, add effective_invoke_separator()
method to IntegrationBase that accepts parsed_options.

CopilotIntegration overrides it to return "-" when skills
mode is requested. The CLI layer simply asks the integration
for its separator — no hasattr or _skills_mode coupling.

Also adds tests for the new method on both base and Copilot,
plus an end-to-end test for 'specify init --integration copilot
--integration-options --skills' verifying page templates get
hyphen refs.
---
 src/specify_cli/__init__.py                   | 42 +++++++++++--------
 src/specify_cli/integrations/base.py          | 12 ++++++
 .../integrations/copilot/__init__.py          | 10 +++++
 tests/integrations/test_base.py               |  7 ++++
 tests/integrations/test_cli.py                | 29 +++++++++++++
 .../integrations/test_integration_copilot.py  | 21 ++++++++++
 6 files changed, 104 insertions(+), 17 deletions(-)

diff --git a/src/specify_cli/__init__.py b/src/specify_cli/__init__.py
index 8d593abefb..1c3e63ec03 100644
--- a/src/specify_cli/__init__.py
+++ b/src/specify_cli/__init__.py
@@ -1305,7 +1305,7 @@ def init(
 
             # Install shared infrastructure (scripts, templates)
             tracker.start("shared-infra")
-            _install_shared_infra(project_path, selected_script, tracker=tracker, force=force, invoke_separator=resolved_integration.invoke_separator)
+            _install_shared_infra(project_path, selected_script, tracker=tracker, force=force, invoke_separator=resolved_integration.effective_invoke_separator(integration_parsed_options))
             tracker.complete("shared-infra", f"scripts ({selected_script}) + templates")
 
             ensure_constitution_from_template(project_path, tracker=tracker)
@@ -2082,9 +2082,16 @@ def integration_install(
 
     selected_script = _resolve_script_type(project_root, script)
 
+    # Build parsed options from --integration-options so the integration
+    # can determine its effective invoke separator before shared infra
+    # is installed.
+    parsed_options: dict[str, Any] | None = None
+    if integration_options:
+        parsed_options = _parse_integration_options(integration, integration_options)
+
     # Ensure shared infrastructure is present (safe to run unconditionally;
     # _install_shared_infra merges missing files without overwriting).
-    _install_shared_infra(project_root, selected_script, invoke_separator=integration.invoke_separator)
+    _install_shared_infra(project_root, selected_script, invoke_separator=integration.effective_invoke_separator(parsed_options))
     if os.name != "nt":
         ensure_executable_scripts(project_root)
 
@@ -2092,11 +2099,6 @@ def integration_install(
         integration.key, project_root, version=get_speckit_version()
     )
 
-    # Build parsed options from --integration-options
-    parsed_options: dict[str, Any] | None = None
-    if integration_options:
-        parsed_options = _parse_integration_options(integration, integration_options)
-
     try:
         integration.setup(
             project_root, manifest,
@@ -2366,9 +2368,16 @@ def integration_switch(
         opts.pop("context_file", None)
         save_init_options(project_root, opts)
 
+    # Build parsed options from --integration-options so the integration
+    # can determine its effective invoke separator before shared infra
+    # is installed.
+    parsed_options: dict[str, Any] | None = None
+    if integration_options:
+        parsed_options = _parse_integration_options(target_integration, integration_options)
+
     # Ensure shared infrastructure is present (safe to run unconditionally;
     # _install_shared_infra merges missing files without overwriting).
-    _install_shared_infra(project_root, selected_script, invoke_separator=target_integration.invoke_separator)
+    _install_shared_infra(project_root, selected_script, invoke_separator=target_integration.effective_invoke_separator(parsed_options))
     if os.name != "nt":
         ensure_executable_scripts(project_root)
 
@@ -2378,10 +2387,6 @@ def integration_switch(
         target_integration.key, project_root, version=get_speckit_version()
     )
 
-    parsed_options: dict[str, Any] | None = None
-    if integration_options:
-        parsed_options = _parse_integration_options(target_integration, integration_options)
-
     try:
         target_integration.setup(
             project_root, manifest,
@@ -2475,8 +2480,15 @@ def integration_upgrade(
 
     selected_script = _resolve_script_type(project_root, script)
 
+    # Build parsed options from --integration-options so the integration
+    # can determine its effective invoke separator before shared infra
+    # is installed.
+    parsed_options: dict[str, Any] | None = None
+    if integration_options:
+        parsed_options = _parse_integration_options(integration, integration_options)
+
     # Ensure shared infrastructure is up to date; --force overwrites existing files.
-    _install_shared_infra(project_root, selected_script, force=force, invoke_separator=integration.invoke_separator)
+    _install_shared_infra(project_root, selected_script, force=force, invoke_separator=integration.effective_invoke_separator(parsed_options))
     if os.name != "nt":
         ensure_executable_scripts(project_root)
 
@@ -2484,10 +2496,6 @@ def integration_upgrade(
     console.print(f"Upgrading integration: [cyan]{key}[/cyan]")
     new_manifest = IntegrationManifest(key, project_root, version=get_speckit_version())
 
-    parsed_options: dict[str, Any] | None = None
-    if integration_options:
-        parsed_options = _parse_integration_options(integration, integration_options)
-
     try:
         integration.setup(
             project_root,
diff --git a/src/specify_cli/integrations/base.py b/src/specify_cli/integrations/base.py
index 16deb9647a..5222ea4293 100644
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -99,6 +99,18 @@ def options(cls) -> list[IntegrationOption]:
         """Return options this integration accepts. Default: none."""
         return []
 
+    def effective_invoke_separator(
+        self, parsed_options: dict[str, Any] | None = None
+    ) -> str:
+        """Return the invoke separator for the given options.
+
+        Subclasses whose separator depends on runtime options (e.g.
+        Copilot in ``--skills`` mode) should override this method.
+        The default implementation ignores *parsed_options* and returns
+        the class-level ``invoke_separator``.
+        """
+        return self.invoke_separator
+
     def build_exec_args(
         self,
         prompt: str,
diff --git a/src/specify_cli/integrations/copilot/__init__.py b/src/specify_cli/integrations/copilot/__init__.py
index 5c4d0e5410..1b6babfc55 100644
--- a/src/specify_cli/integrations/copilot/__init__.py
+++ b/src/specify_cli/integrations/copilot/__init__.py
@@ -103,6 +103,16 @@ class CopilotIntegration(IntegrationBase):
     # Mutable flag set by setup() — indicates the active scaffolding mode.
     _skills_mode: bool = False
 
+    def effective_invoke_separator(
+        self, parsed_options: dict[str, Any] | None = None
+    ) -> str:
+        """Return ``"-"`` when skills mode is requested, ``"."`` otherwise."""
+        if parsed_options and parsed_options.get("skills"):
+            return "-"
+        if self._skills_mode:
+            return "-"
+        return self.invoke_separator
+
     @classmethod
     def options(cls) -> list[IntegrationOption]:
         return [
diff --git a/tests/integrations/test_base.py b/tests/integrations/test_base.py
index 13218e19b2..948f9c0ddf 100644
--- a/tests/integrations/test_base.py
+++ b/tests/integrations/test_base.py
@@ -210,6 +210,13 @@ def test_invoke_separator_class_attribute(self):
         assert IntegrationBase.invoke_separator == "."
         assert SkillsIntegration.invoke_separator == "-"
 
+    def test_effective_invoke_separator_default(self):
+        """Base classes return invoke_separator regardless of parsed_options."""
+        from .conftest import StubIntegration
+        stub = StubIntegration()
+        assert stub.effective_invoke_separator() == "."
+        assert stub.effective_invoke_separator({"skills": True}) == "."
+
     def test_process_template_resolves_placeholders(self):
         content = "---\ndescription: test\n---\nRun __SPECKIT_COMMAND_PLAN__ now."
         result = IntegrationBase.process_template(
diff --git a/tests/integrations/test_cli.py b/tests/integrations/test_cli.py
index 0df43ac1e1..152c56813c 100644
--- a/tests/integrations/test_cli.py
+++ b/tests/integrations/test_cli.py
@@ -572,3 +572,32 @@ def test_full_init_copilot_resolves_page_templates(self, tmp_path):
         content = plan.read_text(encoding="utf-8")
         assert "/speckit.plan" in content, "Copilot (markdown) should use /speckit.plan"
         assert "__SPECKIT_COMMAND_" not in content
+
+    def test_full_init_copilot_skills_resolves_page_templates(self, tmp_path):
+        """Full CLI init with Copilot --skills produces hyphen refs in page templates."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "init-copilot-skills"
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(app, [
+                "init", str(project),
+                "--integration", "copilot",
+                "--integration-options", "--skills",
+                "--script", "sh",
+                "--no-git",
+                "--ignore-agent-tools",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+
+        assert result.exit_code == 0, f"init failed: {result.output}"
+
+        plan = project / ".specify" / "templates" / "plan-template.md"
+        content = plan.read_text(encoding="utf-8")
+        assert "/speckit-plan" in content, "Copilot --skills should use /speckit-plan"
+        assert "/speckit.plan" not in content, "dot-notation leaked into Copilot skills page template"
+        assert "__SPECKIT_COMMAND_" not in content
diff --git a/tests/integrations/test_integration_copilot.py b/tests/integrations/test_integration_copilot.py
index 688fb9dd8d..d59e42c9ed 100644
--- a/tests/integrations/test_integration_copilot.py
+++ b/tests/integrations/test_integration_copilot.py
@@ -445,6 +445,27 @@ def test_skills_templates_are_processed(self, tmp_path):
             assert "{SCRIPT}" not in content, f"{f.name} has unprocessed {{SCRIPT}}"
             assert "__AGENT__" not in content, f"{f.name} has unprocessed __AGENT__"
             assert "{ARGS}" not in content, f"{f.name} has unprocessed {{ARGS}}"
+            assert "__SPECKIT_COMMAND_" not in content, f"{f.name} has unprocessed __SPECKIT_COMMAND_*__"
+
+    def test_skills_command_refs_use_hyphen(self, tmp_path):
+        """Copilot skills mode must use /speckit-<name> not /speckit.<name>."""
+        copilot = self._make_copilot()
+        created, _ = self._setup_skills(copilot, tmp_path)
+        skill_files = [f for f in created if f.name == "SKILL.md"]
+        assert len(skill_files) > 0
+        for f in skill_files:
+            content = f.read_text(encoding="utf-8")
+            assert "/speckit." not in content, (
+                f"{f.name} contains dot-notation /speckit. reference; "
+                f"skills mode must use /speckit-<name>"
+            )
+
+    def test_skills_mode_invoke_separator(self):
+        """Copilot effective_invoke_separator should reflect skills mode."""
+        copilot = self._make_copilot()
+        assert copilot.effective_invoke_separator() == "."
+        assert copilot.effective_invoke_separator({"skills": True}) == "-"
+        assert copilot.effective_invoke_separator({"skills": False}) == "."
 
     def test_skill_body_has_content(self, tmp_path):
         """Each SKILL.md body should contain template content."""

From 1f4267bd6d798b24801f38f8bb2360d4320aa08f Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Fri, 24 Apr 2026 09:39:59 -0500
Subject: [PATCH 3/4] fix: build_command_invocation preserves full suffix for
 extension commands

Previously rsplit('.', 1)[-1] on 'speckit.git.commit' yielded
just 'commit', producing /speckit.commit instead of
/speckit.git.commit (or /speckit-git-commit for skills).

Fix: strip only the 'speckit.' prefix when present, then join
remaining segments with the appropriate separator.

Updated in IntegrationBase, SkillsIntegration, and
CopilotIntegration. Added tests for extension commands in
build_command_invocation across all three.
---
 src/specify_cli/integrations/base.py          | 13 +++---
 .../integrations/copilot/__init__.py          |  6 +--
 tests/integrations/test_base.py               | 41 +++++++++++++++++++
 .../integrations/test_integration_copilot.py  |  6 +++
 4 files changed, 57 insertions(+), 9 deletions(-)

diff --git a/src/specify_cli/integrations/base.py b/src/specify_cli/integrations/base.py
index 5222ea4293..f3b74b0c05 100644
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -137,11 +137,12 @@ def build_command_invocation(self, command_name: str, args: str = "") -> str:
         agents or ``"/speckit-specify my-feature"`` for skills agents.
 
         *command_name* may be a full dotted name like
-        ``"speckit.specify"`` or a bare stem like ``"specify"``.
+        ``"speckit.specify"``, an extension command like
+        ``"speckit.git.commit"``, or a bare stem like ``"specify"``.
         """
         stem = command_name
-        if "." in stem:
-            stem = stem.rsplit(".", 1)[-1]
+        if stem.startswith("speckit."):
+            stem = stem[len("speckit."):]
 
         invocation = f"/speckit.{stem}"
         if args:
@@ -1351,10 +1352,10 @@ def skills_dest(self, project_root: Path) -> Path:
     def build_command_invocation(self, command_name: str, args: str = "") -> str:
         """Skills use ``/speckit-<stem>`` (hyphenated directory name)."""
         stem = command_name
-        if "." in stem:
-            stem = stem.rsplit(".", 1)[-1]
+        if stem.startswith("speckit."):
+            stem = stem[len("speckit."):]
 
-        invocation = f"/speckit-{stem}"
+        invocation = "/speckit-" + stem.replace(".", "-")
         if args:
             invocation = f"{invocation} {args}"
         return invocation
diff --git a/src/specify_cli/integrations/copilot/__init__.py b/src/specify_cli/integrations/copilot/__init__.py
index 1b6babfc55..8557a4eea1 100644
--- a/src/specify_cli/integrations/copilot/__init__.py
+++ b/src/specify_cli/integrations/copilot/__init__.py
@@ -155,9 +155,9 @@ def build_command_invocation(self, command_name: str, args: str = "") -> str:
         """
         if self._skills_mode:
             stem = command_name
-            if "." in stem:
-                stem = stem.rsplit(".", 1)[-1]
-            invocation = f"/speckit-{stem}"
+            if stem.startswith("speckit."):
+                stem = stem[len("speckit."):]
+            invocation = "/speckit-" + stem.replace(".", "-")
             if args:
                 invocation = f"{invocation} {args}"
             return invocation
diff --git a/tests/integrations/test_base.py b/tests/integrations/test_base.py
index 948f9c0ddf..3b244943b4 100644
--- a/tests/integrations/test_base.py
+++ b/tests/integrations/test_base.py
@@ -170,6 +170,47 @@ def test_setup_copies_shared_templates(self, tmp_path):
             assert f.name.endswith(".md")
 
 
+class TestBuildCommandInvocation:
+    """Tests for build_command_invocation across integration types."""
+
+    def test_base_core_command_dotted(self):
+        i = StubIntegration()
+        assert i.build_command_invocation("speckit.plan") == "/speckit.plan"
+
+    def test_base_core_command_bare(self):
+        i = StubIntegration()
+        assert i.build_command_invocation("plan") == "/speckit.plan"
+
+    def test_base_core_command_with_args(self):
+        i = StubIntegration()
+        assert i.build_command_invocation("plan", "my feature") == "/speckit.plan my feature"
+
+    def test_base_extension_command(self):
+        i = StubIntegration()
+        assert i.build_command_invocation("speckit.git.commit") == "/speckit.git.commit"
+
+    def test_base_extension_command_bare(self):
+        i = StubIntegration()
+        assert i.build_command_invocation("git.commit") == "/speckit.git.commit"
+
+    def test_skills_core_command(self):
+        from specify_cli.integrations import get_integration
+        i = get_integration("codex")
+        assert i.build_command_invocation("speckit.plan") == "/speckit-plan"
+        assert i.build_command_invocation("plan") == "/speckit-plan"
+
+    def test_skills_extension_command(self):
+        from specify_cli.integrations import get_integration
+        i = get_integration("codex")
+        assert i.build_command_invocation("speckit.git.commit") == "/speckit-git-commit"
+        assert i.build_command_invocation("git.commit") == "/speckit-git-commit"
+
+    def test_skills_extension_command_with_args(self):
+        from specify_cli.integrations import get_integration
+        i = get_integration("codex")
+        assert i.build_command_invocation("speckit.git.commit", "fix typo") == "/speckit-git-commit fix typo"
+
+
 class TestResolveCommandRefs:
     """Tests for __SPECKIT_COMMAND_<NAME>__ placeholder resolution."""
 
diff --git a/tests/integrations/test_integration_copilot.py b/tests/integrations/test_integration_copilot.py
index d59e42c9ed..2df4d2d7df 100644
--- a/tests/integrations/test_integration_copilot.py
+++ b/tests/integrations/test_integration_copilot.py
@@ -531,6 +531,12 @@ def test_build_command_invocation_skills_mode(self):
         assert copilot.build_command_invocation("plan") == "/speckit-plan"
         assert copilot.build_command_invocation("plan", "my args") == "/speckit-plan my args"
 
+    def test_build_command_invocation_skills_extension_command(self):
+        copilot = self._make_copilot()
+        copilot._skills_mode = True
+        assert copilot.build_command_invocation("speckit.git.commit") == "/speckit-git-commit"
+        assert copilot.build_command_invocation("git.commit") == "/speckit-git-commit"
+
     def test_build_command_invocation_default_mode(self):
         copilot = self._make_copilot()
         assert copilot.build_command_invocation("plan", "my args") == "my args"

From e564ecd1a917f9feb72944420f75923e4c8264fa Mon Sep 17 00:00:00 2001
From: Manfred Riem <15701806+mnriem@users.noreply.github.com>
Date: Fri, 24 Apr 2026 09:58:34 -0500
Subject: [PATCH 4/4] fix: Copilot dispatch_command() preserves full extension
 command suffix
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

dispatch_command() had the same rsplit('.', 1)[-1] bug as
build_command_invocation() — speckit.git.commit would dispatch
as /speckit-commit instead of /speckit-git-commit in skills
mode, or --agent speckit.commit instead of speckit.git.commit
in default mode.
---
 src/specify_cli/integrations/copilot/__init__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/specify_cli/integrations/copilot/__init__.py b/src/specify_cli/integrations/copilot/__init__.py
index 8557a4eea1..c7456ce7f0 100644
--- a/src/specify_cli/integrations/copilot/__init__.py
+++ b/src/specify_cli/integrations/copilot/__init__.py
@@ -185,8 +185,8 @@ def dispatch_command(
         import subprocess
 
         stem = command_name
-        if "." in stem:
-            stem = stem.rsplit(".", 1)[-1]
+        if stem.startswith("speckit."):
+            stem = stem[len("speckit."):]
 
         # Detect skills mode from project layout when not set via setup()
         skills_mode = self._skills_mode
@@ -199,7 +199,7 @@ def dispatch_command(
                 )
 
         if skills_mode:
-            prompt = f"/speckit-{stem}"
+            prompt = "/speckit-" + stem.replace(".", "-")
             if args:
                 prompt = f"{prompt} {args}"
         else: