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>

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.
               };
             };