fix: read nested bundle URIs from in-memory registry in bundle list --all

[colombod]

Summary

Fixes the display half of microsoft-amplifier/amplifier-support#62.

amplifier bundle list --all showed GitHub URLs for nested bundles even when the parent bundle was overridden to a local path via settings.local.yaml. The nested bundles and dependencies categories read URIs from stale ~/.amplifier/registry.json on disk instead of the in-memory registry that has current overrides applied.

Root Cause

get_bundle_categories() in discovery.py used three inconsistent data sources for its output categories:

Category	Data Source	Reflected Overrides?
Well-Known Bundles	Re-resolved via _find_packaged_bundle()	❌
User-Added Bundles	AppSettings().get_added_bundles()	✅
Nested Bundles	~/.amplifier/registry.json on disk	❌ Stale
Dependencies	~/.amplifier/registry.json on disk	❌ Stale

The default bundle list view (without --all) already correctly reads from the in-memory registry via discovery.find(). The --all view was the only inconsistent path.

Change

Replaced the registry.json file-read block with self._registry.get_state() which returns the in-memory BundleState objects that reflect current session state including local overrides.

Before (read from disk):

registry_path = Path.home() / ".amplifier" / "registry.json"
if registry_path.exists():
    with open(registry_path, encoding="utf-8") as f:
        data = json.load(f)
    for name, bundle_data in data.get("bundles", {}).items():
        entry = {"name": name, "uri": bundle_data.get("uri", "")}
        ...

After (read from in-memory registry):

all_states = self._registry.get_state()
if isinstance(all_states, dict):
    for name, state in all_states.items():
        entry = {"name": name, "uri": state.uri}
        ...

The output format and category logic are preserved exactly — only the data source changes.

Evidence

Diff stats

• amplifier_app_cli/lib/bundle_loader/discovery.py: +25/−33 lines (net reduction — simpler code)
• tests/lib/bundle_loader/test_discovery.py: +146 lines (NEW file, 3 regression tests)

Test results

Suite	Before	After	Delta
amplifier-app-cli full suite	165 passed ✅	168 passed ✅	+3 new, 0 regressions

Note: app-cli tests were run with the local amplifier-foundation checkout (including the companion PR's changes) via uv pip install -e + uv run --no-sync, since BundleState.explicitly_requested is needed at runtime.

New regression tests (TestGetBundleCategoriesNestedURIs)

Test	What it verifies
test_nested_bundles_reflect_in_memory_state	Injected in-memory BundleState entries appear in get_bundle_categories() output with correct URIs
test_stale_persisted_uri_not_used_for_nested_bundles	When registry.json has a git+ URI but in-memory state has been updated to file://, the output reflects the in-memory URI
test_dependencies_reflect_in_memory_state	Dependencies also read from in-memory registry with correct included_by metadata

Companion PR

This is the second of two PRs for issue #62. The companion PR is microsoft/amplifier-foundation#83 which fixes the persistent state in BundleRegistry._load_single(). The foundation PR should merge first (it fixes the persistent state), then this PR (it fixes the display).

Together, both PRs ensure:

1. Foundation: Registry entries are refreshed when bundles reload from different sources
2. App CLI (this PR): bundle list --all reads from refreshed in-memory state, not stale disk data

How to verify end-to-end

After both PRs merge:

1. Add bundle.added.foundation: ../../amplifier-foundation to settings.local.yaml
2. Run any Amplifier session (to trigger bundle loading with the override)
3. Run amplifier bundle list --all
4. Confirm nested bundles show local paths, not git+ GitHub URLs

[sadlilas]

Review: Not approving

We reviewed this alongside the companion foundation PR #83 and are choosing to accept #83 but not this PR.

Foundation PR #83 fixes the root cause: stale URIs in the registry are now corrected during _load_single() on every bundle load. Once #83 is merged, the first session a user runs updates all URIs in memory and persists them to registry.json via registry.save(). After that single session, bundle list --all reads correct URIs from disk permanently.

This PR fixes a one-time display inconsistency that only exists between when the user gets the new code and when they run their first session. It self-heals after one use. That is not enough to justify changing the CLI display code path.

Thank you for the thorough work -- the root cause analysis and foundation fix are the right changes.

[colombod]

Closing the pr