Don't persist ephemeral extensions when resuming sessions

[wpfleger96]

Fixes #5973

Summary

When resuming sessions with ephemeral extensions (added via --with-extension) or recipe extensions, they should be restored for the session only, not permanently saved to config. Otherwise the user ends up with a duplicate garbage extension entry in ~/.config/goose/config.yaml:

goose session --with-extension "uvx mcp_gdrive@latest"
# ... do work, exit session ...

goose session --resume --session-id <id>
# Prompt: "Extension(s) mcpgdrive_sgoMpj77 from previous session are no longer in config. Re-add them to config?"
# Answer: Yes

now ~/.config/goose/config.yaml has:

  mcpgdrivelatest_gbtrm2lw:
    enabled: true
    type: stdio
    name: mcpgdrivelatest_gBtrm2lw
    description: ''
    cmd: uvx
    args:
    - mcp_gdrive@latest
    envs: {}
    env_keys: []
    timeout: 300
    bundled: null
    available_tools: []

Changes

• Updated prompt message: "Restore for this session?" (was "Re-add them to config?")
• Removed set_extension() call that wrote to config.yaml
• Cleaned up unused imports

Root cause

check_missing_extensions_or_exit() called set_extension() which writes to config.yaml. Unnecessary since extensions are already restored from saved_state.extensions.

[Copilot]

Pull request overview

This PR fixes a bug where ephemeral extensions (added via --with-extension or from recipes) were incorrectly being persisted to config.yaml when resuming sessions. The fix removes the unnecessary set_extension() call that was writing to the config file, while preserving the correct behavior of restoring extensions from saved session state.

Key Changes:

• Updated the user-facing prompt to clarify that extensions are restored "for this session" rather than permanently
• Removed the set_extension() call that incorrectly persisted extensions to config.yaml
• Cleaned up unused imports (set_extension, ExtensionEntry)