fix: scaffold extension config when installing via bundler

[chelsealong]

Summary

Fixes #4283.

specify bundle install installs an extension by calling
ExtensionManager.install_from_directory / install_from_zip directly
from _ExtensionKindManager._do_install in
src/specify_cli/bundler/services/primitives.py, but never called
ExtensionManager.scaffold_config afterwards. The specify extension add
command flow (src/specify_cli/extensions/_commands.py) does call it, so
an extension installed as part of a bundle ended up with its
provides.config templates present on disk but never deployed — the
extension silently had no configuration, while installing the same
extension directly worked correctly.

Change

• src/specify_cli/bundler/services/primitives.py: call
  self._manager.scaffold_config(manifest.id) right after a successful
  install_from_directory/install_from_zip call in
  _ExtensionKindManager._do_install, using the id from the manifest
  returned by the install call (matching what the extension add command
  flow does).
• tests/unit/test_bundler_primitives.py: added
  test_bundled_extension_install_scaffolds_config, which installs a real
  (unmocked) extension source with a provides.config entry through
  primitive_manager("extensions", ...) and asserts the config file lands
  at .specify/extensions/<id>/<name>. Also updated the existing
  install_from_directory mocks in this file to return an object with an
  .id attribute (as the real method does), since the new call site reads
  manifest.id off the return value.

Out of scope: the issue's related documentation nit about
_target_follows_preserved_convention naming conventions not being
documented in EXTENSION-API-REFERENCE.md, and surfacing per-file
deployed/skipped/failed console reporting through the bundler's CLI
summary (the bundler currently reports install results only as install
counts, not per-component detail — plumbing that through is a larger,
separate change).

Test plan

Confirmed the new test fails without the fix (temporarily reverted just
the production file):

$ git stash push -- src/specify_cli/bundler/services/primitives.py
$ python3 -m uv run pytest tests/unit/test_bundler_primitives.py -q
...
FAILED tests/unit/test_bundler_primitives.py::test_bundled_extension_install_scaffolds_config - AssertionError: assert False
 +  where False = exists()
 +    where exists = PosixPath('.../project/.specify/extensions/my-ext/my-ext-config.yml').exists
1 failed, 20 passed in 0.28s
$ git stash pop

With the fix:

$ python3 -m uv run pytest tests/unit/test_bundler_primitives.py -q
21 passed in 0.27s

Full suite (unmodified elsewhere):

$ python3 -m uv run pytest -q
7309 passed, 10 skipped, 48 warnings in 467.66s

ruff check on the touched files reports 4 pre-existing issues (unused
noqa on lines untouched by this change, import-order in two unrelated
test functions) that are also present on unmodified upstream/main —
confirmed by stashing this change and re-running the same ruff check
invocation, which reported the identical 4 findings at the same
locations.

AI disclosure

This change was implemented with AI assistance (Claude Code), including
the fix, the regression test, and this PR description. All commands
listed above were run and their output verified directly.

[Copilot]

Pull request overview

Fixes bundle-installed extensions failing to scaffold declared configuration templates.

Changes:

• Scaffolds config after directory and ZIP installs.
• Adds bundled-directory regression coverage.
• Updates mocks to return manifest IDs.

Show a summary per file

File	Description
src/specify_cli/bundler/services/primitives.py	Scaffolds extension config after installation.
tests/unit/test_bundler_primitives.py	Adds regression coverage and updates mocks.

Review details

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• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Balanced

[KSchlobohm]

Please add a regression test for the catalog/ZIP install path. The current test covers only an extension already bundled with Spec Kit, while the reported reproduction uses an extension downloaded from the catalog. The new test should confirm that installing the downloaded ZIP creates the extension's configuration file. Once updated, we'll take another look.

[chelsealong]

Added test_catalog_extension_install_scaffolds_config in tests/unit/test_bundler_primitives.py, which forces the catalog/ZIP branch (_locate_bundled_extension returns None, ExtensionCatalog.download_extension supplies a real ZIP built from an extension with a provides.config entry) and asserts the scaffolded config file lands on disk. Confirmed it fails without the fix and passes with it; full suite (7310 passed) and ruff on touched files are unchanged from before (same 4 pre-existing findings noted in the PR description).