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/BACKLOG.md

@@ -37,10 +37,10 @@ generation the ISO pins for offline installs contains the chromium binary,
 `chromium-browser.desktop`, and all three HTTP/HTML handlers
 (mime.nix sets them; template ships the package). The Acer sighting is the
 LIVE session, which ships NO browser by design (mime defaults name chromium,
-GIO skips it while absent) — #103 adds live baseline apps. Remains: a
-test-install VM run proving chromium launches post-install (chain #97's
-Bluetooth-click V2 into the same run), + make the live posture explicit in
-the flake comment (edit drafted, uncommitted).
+GIO skips it while absent) — #103 adds live baseline apps. Live posture is
+now explicit in the flake comment. Remains: a test-install VM run proving
+chromium launches post-install (chain #97's Bluetooth-click V2 into the
+same run).
 
 Chromium is the resolved default-browser decision and is present in the
 downstream template, but this hardware pass found no usable default browser.
@@ -71,26 +71,27 @@ buttons in the installer (VM gum screens under Boreal look legible —
 artifacts in `/tmp/nomarchy-v2-swap-93/`). Needs Bernardo's screenshot or
 an Acer repro to pin the actual widget before fixing.
 
-### 99. Doctor/Waybar reports `theme.json` is not git-tracked
+### 113. Live session: offline theme switch rebuilds the world from source
 
-**Progress 2026-07-13:** root-caused — the message is doctor's
-"`theme-state.json` is NOT git-tracked": the live seed (hosts/live.nix
-`nomarchy-seed-flake`) does `cp -r` with no `git init`, so `~/.nomarchy`
-isn't a repo in the LIVE session (installed systems commit at
-nomarchy-install.sh:654 and are fine). Fix drafted in the working tree
-(seed does init+add+commit like the installer). Held for one open
-question: the same evidence run saw the live offline
-`nomarchy-theme-sync apply gruvbox` rebuild fail ("Build failed due to
-failed dependency") — determine whether that predates the git-seed (the
-git+file eval flips untracked-file visibility) before committing; a
-focused VM run capturing the full rebuild log over serial is in flight
-(`/tmp/nomarchy-v2-theme-99/`).
-
-The live-installed checkout shows a doctor/Waybar warning that `theme.json`
-is not tracked. Determine whether the warning targets the generated alias or
-the canonical `theme-state.json`, then align the check with the in-flake state
-contract. Pass = a fresh install has no false warning while a genuinely
-untracked canonical state file is still detected.
+Surfaced by #99's evidence run (2026-07-13, `/tmp/nomarchy-v2-theme-99/`):
+in the **live ISO** session, offline `nomarchy-theme-sync apply gruvbox`
+fails — its `home-manager switch` tries to build **1176 derivations** from
+the `stage0`/`hex0` bootstrap up, then dies on offline source fetches
+(`vala`, `yasm`, `config.jsonc`, `ghostty-config`, `easyeffects.svg`,
+`typogrify`…), ending `error: Build failed due to failed dependency`. This
+contradicts docs/TESTING.md item 6 ("apply gruvbox → switch runs offline").
+The failing generation is `bvl30ggn…-home-manager-generation.drv`; it is
+**not** the drv the ISO pins (the pin is the *default*-theme
+`homeConfigurations.${username}.activationPackage`, i.e. Boreal — confirmed
+drv-identical to the failing one only for gruvbox state, so a non-default
+theme's generation is unpinned). NOT caused by #99's git-seed: the drv is
+byte-identical path-seeded vs git-seeded. **Decide the contract:** either
+pin every baked theme's live activationPackage into the ISO (size cost) or
+scope the offline-switch promise to the shipped theme + correct
+TESTING.md/MEMORY. Pass = a fresh live ISO either switches to any baked
+theme offline, or fails with a clear "needs network for this theme" message
+and accurate docs. **Not caused by anything in today's batch** — separate
+pre-existing ISO-pinning gap.
 
 ## NEXT
 

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

flake.nix

@@ -1572,6 +1572,13 @@
               users.${username} = {
                 imports = [ self.homeModules.nomarchy ];
                 nomarchy.stateFile = ./theme-state.json;
+                # Deliberate live-session posture (BACKLOG #94): the live
+                # desktop ships the distro modules only — NO browser or
+                # template app suite (mime defaults still name chromium,
+                # which GIO skips while absent). The template's Chromium +
+                # apps arrive with installation (the ISO pins that HM
+                # closure for offline installs); #103 adds a baseline app
+                # set to the live session itself.
               };
             };
 

hosts/live.nix

@@ -148,6 +148,16 @@ in
       if [ ! -e "$home/.nomarchy" ]; then
         cp -r ${nomarchySrc} "$home/.nomarchy"
         chmod -R u+w "$home/.nomarchy"
+        # Committed git repo, exactly like nomarchy-install produces —
+        # otherwise nomarchy-doctor (and its Waybar badge) false-alarms
+        # "theme-state.json is NOT git-tracked" in the live session.
+        (
+          cd "$home/.nomarchy"
+          ${pkgs.git}/bin/git init -q
+          ${pkgs.git}/bin/git add -A
+          ${pkgs.git}/bin/git -c user.name="Nomarchy Live" -c user.email="live@nomarchy" \
+            commit -qm "Nomarchy live session"
+        )
         chown -R ${username}:users "$home/.nomarchy"
       fi
     '';