[BUG] prune marks a declared GitHub package orphaned after a casing-only manifest change

Describe the bug

In APM 0.31.0, changing only the GitHub owner/repository casing in a dependency declaration causes apm prune --dry-run to classify the installed package as orphaned.

To Reproduce

1. With APM 0.31.0, create this manifest and run apm install:

   name: prune-fixture
   version: 1.0.0
   targets:
     - agent-skills
   dependencies:
     apm:
       - microsoft/apm#v0.31.0
     mcp: []
   

2. Confirm that the package is materialized at apm_modules/microsoft/apm.

3. Change only microsoft/apm to Microsoft/APM in the dependency declaration:

   dependencies:
     apm:
       - Microsoft/APM#v0.31.0
   

4. Run apm prune --dry-run without reinstalling:

   [>] Analyzing installed packages vs apm.yml...
   [!] Found 1 orphaned package(s):
   [!]   - microsoft/apm (would be removed)
   [*] Dry run complete - no changes made
   

Expected behavior

The existing package is recognized as the declared GitHub dependency. Changing GitHub owner/repository casing does not change package identity or make the package orphaned.

Environment (please complete the following information):

• OS: macOS
• Python Version: 3.14.7
• APM Version: 0.31.0 (Homebrew); also reproduced with current main
• VSCode Version (if relevant): Not applicable

Logs

The complete relevant output is included in the reproduction above.

Additional context

GitHub package identity is normalized to lowercase, while materialization paths preserve source casing. Prune compares expected and scanned materialization paths directly.

This is distinct from #3015: that report concerns a genuine orphan not being detected; this report concerns a declared package being falsely detected as orphaned.

Start in src/apm_cli/commands/prune.py at the expected-versus-scanned materialization path comparison, then read the normalization logic in src/apm_cli/models/dependency/identity.py and path handling in src/apm_cli/models/dependency/materialization.py. Reproduce the casing-only manifest change and verify that apm prune --dry-run recognizes the existing package rather than reporting it as orphaned.