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.

6 files changed, 10 insertions, 3 deletions

diff --git a/modules/calendar-sync.el b/modules/calendar-sync.el
index 62d1b5f1..f0d6f786 100644
--- a/modules/calendar-sync.el
+++ b/modules/calendar-sync.el
@@ -167,7 +167,7 @@ Hash table mapping calendar name (string) to state plist with:
 Used to detect timezone changes (e.g., when traveling).")
 
 (defvar calendar-sync--state-file
-  (expand-file-name "data/calendar-sync-state.el" user-emacs-directory)
+  (expand-file-name "persist/calendar-sync-state.el" user-emacs-directory)
   "File to persist sync state across Emacs sessions.")
 
 ;;; Timezone Detection
diff --git a/modules/chrono-tools.el b/modules/chrono-tools.el
index 8b8c2072..33f2b11e 100644
--- a/modules/chrono-tools.el
+++ b/modules/chrono-tools.el
@@ -18,6 +18,9 @@
 (use-package time-zones
   :defer
   :commands time-zones
+  :init
+  (setq time-zones--city-list-file
+        (expand-file-name "persist/time-zones-cities.el" user-emacs-directory))
   :bind ("M-S-c" . time-zones))  ;; was M-C, overrides capitalize-word
 
 (use-package calendar
diff --git a/modules/org-config.el b/modules/org-config.el
index 20160d7d..c04683c0 100644
--- a/modules/org-config.el
+++ b/modules/org-config.el
@@ -25,6 +25,8 @@
   (setq org-startup-folded t)               ;; all org files should start in the folded state
   (setq org-cycle-open-archived-trees t)    ;; re-enable opening headings with archive tags with TAB
   (setq org-cycle-hide-drawers 'all)        ;; collapse :PROPERTIES: drawers when a heading folds
+  (setq org-id-locations-file
+        (expand-file-name "persist/org-id-locations" user-emacs-directory))
   (setopt org-outline-path-complete-in-steps nil)
   (setq org-return-follows-link t)          ;; hit return to follow an org-link
   (setq org-list-allow-alphabetical t)      ;; allow alpha ordered lists (i.e., a), A), a., etc.)
diff --git a/modules/pdf-config.el b/modules/pdf-config.el
index 3835eaa8..cc32f62b 100644
--- a/modules/pdf-config.el
+++ b/modules/pdf-config.el
@@ -65,7 +65,7 @@
   :hook
   (pdf-view-mode . pdf-view-restore-mode)
   :config
-  (setq pdf-view-restore-filename (concat user-emacs-directory "/.pdf-view-restore")))
+  (setq pdf-view-restore-filename (expand-file-name "persist/pdf-view-restore" user-emacs-directory)))
 
 (provide 'pdf-config)
 ;;; pdf-config.el ends here.
diff --git a/modules/selection-framework.el b/modules/selection-framework.el
index 2a714866..15ef0a94 100644
--- a/modules/selection-framework.el
+++ b/modules/selection-framework.el
@@ -229,6 +229,8 @@
 
 (use-package prescient
   :demand t
+  :custom
+  (prescient-save-file (expand-file-name "persist/prescient-save.el" user-emacs-directory))
   :config
   (prescient-persist-mode))
 
diff --git a/modules/ui-theme.el b/modules/ui-theme.el
index f84d7231..bcc58575 100644
--- a/modules/ui-theme.el
+++ b/modules/ui-theme.el
@@ -48,7 +48,7 @@ Unloads any other applied themes before applying the chosen theme."
   "Theme persistence settings."
   :group 'faces)
 
-(defcustom theme-file (expand-file-name ".emacs-theme" user-emacs-directory)
+(defcustom theme-file (expand-file-name "persist/emacs-theme" user-emacs-directory)
   "The location of the file to persist the theme name.
 If you want your theme change to persist across instances, put this in a
 directory that is sync'd across machines with this configuration."