Name patterns the IDE treats as nonexistent (.DS_Store, __pycache__, *.pyc, VCS dirs, ...) were hard-coded in five places, and Git changes ignored none of them, so .DS_Store showed up as unversioned. files.ignoredNames (IDEA's default list) now drives the project view, navigation bar, index, watcher, Find in Files, inspections and the Git status.
Opening another project in the same window left the previous project's state in
module-level stores: Amend and the commit message carried over, debug sessions kept
running, and Git Log, usages, hierarchy, inspection, HTTP client, recent locations,
navigation history and notifications still showed the old project.
Reset each of them on a project root change, stop the old debug sessions, ask about
unsaved changes before leaving a project, close the settings window (it would apply
to the new project) and end the indexing task when a scan is cancelled.