bundle add with #subdirectory --app registers the root bundle too; removing the added entry doesn't undo the add

Bug

amplifier bundle add "git+https://…/repo@main#subdirectory=behaviors/x.yaml" --app registers two entries — the requested behavior and the repo's root bundle (status app). Removing the behavior entry alone does not undo the add: the root bundle's config stays active. Adopters reasonably conclude removal is broken.

Repro (DTU, 2026-09-02)

amplifier bundle add "git+https://github.com/microsoft/amplifier-bundle-converge@main#subdirectory=behaviors/converge.yaml" --app
amplifier bundle list        # shows BOTH: converge-behavior (app) AND converge (app)
amplifier bundle remove converge-behavior
# effects of the add persist — the root bundle's top-level config (at the time,
# a spawn: block in bundle.md) kept applying to every session
amplifier bundle remove converge
# only now does behavior return to baseline (verified byte-identical tool lists)

Observed while validating an adopter report against amplifier-bundle-converge (that bundle's session-wide spawn: block is itself now removed — this issue is about the registration/removal asymmetry, which reproduces independent of what the root config contains).

Expected

Either (a) a #subdirectory= add registers only the requested bundle, or (b) bundle remove <name> removes everything the corresponding add created — one add, one remove, symmetric. If the root registration is intentional (e.g. for namespace: resolution), it should not be composed as an app entry, and bundle list + removal messaging should make the pairing explicit.

Start by reproducing the behavior with amplifier bundle add, amplifier bundle list, and amplifier bundle remove using the subdirectory URL in the issue. Trace the registration and removal paths to determine how the requested bundle and root bundle are paired. Done means one add has symmetric removal, with bundle list and removal behavior making any intentional pairing explicit.