fix(live): git-init the seeded flake so doctor stops false-warning

BACKLOG #99: the live-session seed (nomarchy-seed-flake) did a bare
`cp -r` with no `git init`, so `~/.nomarchy` was not a repo in the live
session and nomarchy-doctor's `git ls-files --error-unmatch
theme-state.json` false-alarmed "theme-state.json is NOT git-tracked"
(installed systems commit at nomarchy-install.sh:654 and were always
fine). The seed now init+add+commits, exactly like the installer.

Verified: V2 — focused serial-log VM run
(/tmp/nomarchy-v2-theme-99/): doctor prints "theme-state.json is
git-tracked" and "flake checkout is clean"; GIT_REPO_OK / TRACKED_OK
markers. A drv-equivalence test proves the seed change is
build-neutral: homeConfigurations.<user>.activationPackage is
byte-identical path-seeded vs git-seeded
(bvl30ggn...-home-manager-generation.drv). nix flake check green.

The same run exposed a separate, pre-existing failure — offline theme
switching in the live session rebuilds from source and dies offline —
filed as BACKLOG #113 (NOT caused by this change: same drv either way).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

agent/JOURNAL.md

@@ -19,19 +19,24 @@ Template:
 
 ---
 
-## 2026-07-13 — session wrap: #94/#98/#99 parked with findings (this commit)
-- **Task:** Record in-progress state (token budget wrap-up).
-- **Did:** BACKLOG progress notes on #94 (installed chromium path V1-proven;
-  live posture is the real gap), #98 (not palette-level; needs the actual
-  widget identified), #99 (root cause + fix drafted; held on the open live
-  offline theme-switch failure — focused serial-log VM run in flight to
-  `/tmp/nomarchy-v2-theme-99/`).
-- **Verified:** V0 — notes only. Working tree deliberately carries two
-  uncommitted drafts: hosts/live.nix git-seed (#99) and the flake.nix live
-  posture comment (#94); next session verifies then commits or reverts.
-- **Pending:** #99 decision from the in-flight run; #94 test-install run
-  (+ #97 V2 click); #96 V3 + #101 round 2 in HARDWARE-QUEUE.
-- **Next suggestion:** read the #99 run's serial.log first.
+## 2026-07-13 — #99 live-seed git-init; theme-switch failure filed as #113 (this commit)
+- **Task:** BACKLOG #99 — false "theme-state.json NOT git-tracked" doctor/
+  Waybar warning in the live session; resolve the held question from Fable.
+- **Did:** hosts/live.nix `nomarchy-seed-flake` now `git init`+`add`+`commit`s
+  the seeded `~/.nomarchy` (like nomarchy-install.sh:654), so the live
+  checkout is a committed repo. Also committed #94's live-posture comment in
+  flake.nix (separate commit).
+- **Verified:** V2 — focused serial-log VM run (`/tmp/nomarchy-v2-theme-99/`):
+  doctor prints `✔ theme-state.json is git-tracked` + `✔ flake checkout is
+  clean`, `GIT_REPO_OK`/`TRACKED_OK` markers. Held question RESOLVED: the
+  same run's offline gruvbox switch failed with a 1176-drv source rebuild,
+  but a local drv-equivalence test proved the failing
+  `bvl30ggn…home-manager-generation.drv` is BYTE-IDENTICAL path-seeded vs
+  git-seeded → the git-seed is exonerated; the failure is a pre-existing
+  ISO-pinning gap (unpinned non-default-theme generation), now filed as #113.
+- **Pending:** #113 (offline theme-switch contract); #94 launch check; #97
+  V2 click; #96 V3 + #101 round 2 (HARDWARE-QUEUE).
+- **Next suggestion:** #113 — decide pin-all-themes vs scope the offline promise.
 
 ## 2026-07-13 — #96+#97 menu gates explain instead of vanish/raw-fail (this commit)
 - **Task:** BACKLOG #96 (battery-limit row silently absent on threshold-less