fix(activator): install a bundle root's package only when a declared module lives there; fail by name

[Brian Krabach (bkrabach)]

Defect

Bundle.prepare() editable-installed the root Python package of the composed bundle and of every included bundle whenever the root pyproject.toml carried a [project] table (ModuleActivator.activate_bundle_package). That inference is wrong for a class of repos it never anticipated: a Python application that ships a skills-only behavior. Its [project] table is the application, no declared module imports from it — and because --app bundles are an include of every session, one amplifier bundle add of such a repo made every session on the machine fail at preparation (uv pip install -e <app root> refused: requires-python >= 3.13 vs the fresh-install venv's 3.12.3), attributed to whichever bundle happened to be loading (Failed to load bundle 'anchors'). On a 3.13 host it would instead silently install the whole application into the consumer's Amplifier environment. Reproduced end-to-end in a clean container; bundle remove was the only cure. Related to the #326-era _distribution_installed skip, which mitigated a sibling manifestation of the same heuristic.

Fix

• activate_bundle_package(bundle_path, progress_callback=None, *, module_sources=None) — when module_sources is given, the package is installed only if at least one declared module source resolves inside the bundle root (bundle_root_declares_module): a local path (relative sources are already absolute by prepare() time), or a git+ source whose repo+ref hash to the same cache directory as the root — the git handler's own placement computation, so a same-repo #subdirectory=modules/x matches and any other repo does not. None preserves the historical rule for callers that cannot supply the list.
• Bundle.prepare() collects modules_to_activate first and passes the declared sources to every root-package install. The bundle's own root failing propagates; an included root failing honors strict exactly as module activation does — raise under strict, otherwise skip with a warning naming the include and let any module that truly needed it fail on its own, by name, in activate_all().
• BundlePackageInstallError(BundleError) names the owning bundle root and package (and points at bundle remove); a requires-python that excludes the running interpreter is reported in one sentence before uv is spawned (best-effort via packaging, not a declared dependency — skipped if absent).

Verification

• 20 new tests (tests/test_activate_bundle_package.py): inference in isolation (same-repo git / other repo / different ref / garbage), install decision, attribution, and the prepare() call site including the exact field shape under strict=True. Full suite 1716 passed, 1 skipped; zero new ruff findings.
• Clean-environment A/B (two DTU containers, one differing input): stock foundation → adding the app-repo behavior breaks every session (Error mounting tools … Python>=3.13); with this branch resolved as the dependency by a fresh uv tool install amplifier (direct_url.json commit d2a7bd9) → sessions work, the three shipped skills load, and the positive control still holds: adding amplifier-bundle-recipes still editable-installs amplifier-recipe-runner from the bundle cache root (its module lives in its own repo).

Not exercised live: a Python 3.13 host (unit-tested only).

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