Lab: swamp repo upgrade deletes extension model source files

Description

Running swamp repo upgrade in a repository containing a published extension deleted the extension model source files from the working tree without warning.

Steps to Reproduce

Have a swamp repository with a custom extension model in extensions/models/ (e.g. launchd_daemon.ts and supporting _lib/ files)
Run swamp repo upgrade
Observe that extension model .ts files are deleted from the working tree (shown as deleted: in git status)

Expected Behavior

swamp repo upgrade should only update swamp-managed scaffolding (CLAUDE.md, .swamp.yaml, etc.) and leave user-authored extension source files untouched.

Actual Behavior

The following files were deleted from extensions/models/:

launchd_daemon.ts (the extension model entrypoint)
_lib/launchctl.ts
_lib/plist.ts
_lib/vendor.ts

Files were recoverable via git restore since they were committed, but the upgrade gave no warning before deleting them.

Environment

swamp version: 20260424.000956.0-sha.25668e08
OS: macOS 26.4.1
Shell: zsh

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