update(source) unconditionally called updateSourceForScope for both
user and project scopes, creating a local install even when the source
was only registered globally. Unify into a single code path that
iterates settings per scope, filtering by identity when a source is
provided.
Tests used setExtensionPaths but update() iterates packages, not
extensions. All 5 non-pinned tests were silently passing as no-ops.
Also add regression test for scope-aware update behavior.
When creating a new session, initial model and thinking level were set
on the agent but never saved to session file. This caused --resume to
default thinking level to 'off'.
fixes#342
Aliou Diallo