[Bug]: Extension alias conflict check misses spellings that map to the same file, so one extension overwrites and then deletes another's alias #5081

Bug Description

_validate_install_conflicts normalises declared names with _normalize_shadow_name only when comparing them with core commands. Against installed extensions it uses an exact spelling check (if name in installed_names, src/specify_cli/extensions/__init__.py:1240). Aliases such as shared.sync and shared-sync both render to .claude/skills/speckit-shared-sync/SKILL.md, so a second extension is installed without error and overwrites the first extension's alias file. Removing the second extension then deletes that file, although the first extension is still installed.

Steps to Reproduce

Save this as repro.py and run uv run python -I repro.py from the repository root.

import os, tempfile
from pathlib import Path
from typer.testing import CliRunner
from specify_cli import app

root = Path(tempfile.mkdtemp())
def make_ext(eid, alias):
    d = root / eid
    (d / "commands").mkdir(parents=True)
    (d / "commands/hello.md").write_text(f"---\ndescription: {eid}\n---\n\nHello from {eid}\n")
    (d / "extension.yml").write_text(f"""schema_version: "1.0"
extension: {{id: {eid}, name: {eid}, version: 1.0.0, description: d}}
requires: {{speckit_version: ">=0.1.0"}}
provides:
  commands:
    - name: speckit.{eid}.hello
      file: commands/hello.md
      description: x
      aliases: ["{alias}"]
""")
    return d
proj = root / "project"
(proj / ".specify").mkdir(parents=True)
(proj / ".claude/skills").mkdir(parents=True)
os.chdir(proj)
run = lambda *a: CliRunner().invoke(app, list(a))
skill = proj / ".claude/skills/speckit-shared-sync/SKILL.md"

print("add alpha:", run("extension", "add", "--dev", str(make_ext("alpha", "shared.sync"))).exit_code)
print("skill belongs to alpha:", "alpha" in skill.read_text())
print("add beta:", run("extension", "add", "--dev", str(make_ext("beta", "shared-sync"))).exit_code)
print("skill belongs to beta:", "beta" in skill.read_text())
print("remove beta:", run("extension", "remove", "beta", "--force").exit_code)
print("alpha still installed:", "alpha" in run("extension", "list").output)
print("alpha's alias skill exists:", skill.exists())

Expected Behavior

specify extension add --dev for beta fails with a conflict error. The _validate_install_conflicts docstring says "Reject installs that would shadow core or installed extension commands" (__init__.py:1220). The _normalize_shadow_name docstring (__init__.py:1203-1216) notes that dotted and hyphenated spellings "land on the same on-disk command name".

Actual Behavior

add alpha: 0
skill belongs to alpha: True
add beta: 0
skill belongs to beta: True
remove beta: 0
alpha still installed: True
alpha's alias skill exists: False

Specify CLI Version

1.2.4.dev0 (main at 27d14e2)

AI Agent

Claude Code

Operating System

Linux 6.18 (Ubuntu container)

Python Version

Python 3.12.3

Additional Context

Comparing _normalize_shadow_name(name) against the normalised installed names, as is already done for core commands, would catch this.

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.