refactor: consolidate runtime state into persist/

Six previously-scattered runtime state files now live under persist/
in user-emacs-directory:

- theme-file (was .emacs-theme)
- pdf-view-restore-filename (was .pdf-view-restore)
- time-zones--city-list-file (was .time-zones.el)
- calendar-sync--state-file (was data/calendar-sync-state.el)
- prescient-save-file (was var/prescient-save.el)
- org-id-locations-file (was .org-id-locations)

The defaults in each module now expand to persist/<name> instead of
the user-emacs-directory root or ad-hoc subdirs.  Existing files
moved into persist/ alongside this change so the next launch picks
up the state without regenerating.

test-ui-theme-default-theme-file-is-emacs-dotfile renamed to
test-ui-theme-default-theme-file-is-under-persist and updated to
assert the new default path.

lsp-session-file is left at the root for now -- prog-lsp.el has no
(require) reference anywhere, so the use-package block that would
carry the redirect never runs.  Tier 3 follow-up: confirm the module
is dead, then delete it or wire it into the load chain.

The var/ directory is now empty and removed.  data/ retains the
calendar agenda content (dcal/gcal/pcal.org) and the .rest API
examples -- content, not state, stays where it is.

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