diff --git a/FORK.md b/FORK.md
index 228e00133c..f4c0811a2c 100644
--- a/FORK.md
+++ b/FORK.md
@@ -11,7 +11,7 @@ All files listed below are modified from upstream and will likely conflict on me
 | Package name | `specify-cli` → `specify-af-cli` | `pyproject.toml` |
 | Binary name | `specify` → `specify-af` | `pyproject.toml` |
 | Catalog URL | Points at `appfolio/spec-kit` `af-main` branch | `src/specify_cli/extensions.py`, `extensions/catalog.json` |
-| Init flow | Auto-installs bundled AF extensions after scaffold. `--force` now overwrites init-managed files (scripts, templates, extensions, skills) while preserving user content (`memory/`, `feature.json`, `semantic-specs/`). Cleans up stale `.claude/commands/speckit.*.md` files from pre-fork installs | `src/specify_cli/__init__.py`, `src/specify_cli/integrations/claude/__init__.py` |
+| Init flow | Auto-installs bundled AF extensions after scaffold. `--force` now overwrites init-managed files (scripts, templates, extensions, skills) while preserving user content (`memory/`, `feature.json`, `semantic-specs/`). Cleans up stale `.claude/commands/speckit.*.md` files from pre-fork installs and known-removed AF skill dirs under `.claude/skills/` (e.g. `speckit-af-check-version`, `speckit-af-after-common`) which Claude Code would otherwise auto-discover and use to hijack lifecycle dispatch | `src/specify_cli/__init__.py`, `src/specify_cli/integrations/claude/__init__.py` |
 | Removed command | `specify-af upgrade` removed — redundant with reinit flow | `src/specify_cli/__init__.py` |
 | Version resolution | Uses `packages_distributions()` instead of hardcoded package name | `src/specify_cli/__init__.py` |
 | Release workflow | release-please with `af-v*` tags on `af-main` | `.github/workflows/release.yml` |
diff --git a/src/specify_cli/integrations/claude/__init__.py b/src/specify_cli/integrations/claude/__init__.py
index 90859ba8cc..f98008ca38 100644
--- a/src/specify_cli/integrations/claude/__init__.py
+++ b/src/specify_cli/integrations/claude/__init__.py
@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import shutil
 from pathlib import Path
 from typing import Any
 
@@ -166,6 +167,24 @@ def setup(
             for stale in commands_dir.glob("speckit.*.md"):
                 stale.unlink()
 
+        # Clean up legacy AF skill directories that were shipped in earlier
+        # versions of the fork but have since been removed or consolidated.
+        # --force only overwrites current files; directories whose matching
+        # bundle content no longer exists survive unless explicitly pruned.
+        # Claude Code auto-discovers these via skill descriptions, which can
+        # hijack lifecycle dispatch (e.g. a stale speckit-af-check-version
+        # skill intercepts VERSION_FAIL handling that now lives in common.md).
+        legacy_af_skills = (
+            "speckit-af-check-version",  # replaced by inline VERSION_FAIL branch in common.md
+            "speckit-af-after-common",    # never had a SKILL.md; empty dir leftover
+        )
+        skills_root = project_root / ".claude" / "skills"
+        if skills_root.is_dir():
+            for legacy in legacy_af_skills:
+                legacy_dir = skills_root / legacy
+                if legacy_dir.is_dir():
+                    shutil.rmtree(legacy_dir)
+
         # Post-process generated skill files
         skills_dir = self.skills_dest(project_root).resolve()