Refuse before anything of the user's is touched, whatever state the runtime is in

The refusals that leave a self-installed Hermes alone came before the command was replaced only for a finished runtime. An unfinished one was still bootstrapped over a git status that could not be read, since a failed status read as a clean tree, and a half-built app beside it, or an edit the Linux runtime patch could not land on, was found only after the user's command had been saved aside and replaced and main switched. All three are asked first now, in both states, so a run that is going to stop leaves the launcher, the checkout and ~/.local/bin as they were.

Co-Authored-By: Codex XHigh <noreply@openai.com>
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>

bin/omarchy-install-hermes-cli

@@ -368,19 +368,24 @@ if runtime_ready; then
   runtime_present=true
 fi
 
+# A seeded app has to be whole, whatever state the runtime beside it is in.
+refuse_unless_app_whole() {
+  if [[ -e $native_app || -L $native_app ]] && ! native_app_complete; then
+    echo "The Hermes desktop app at $native_app is incomplete. Repair it with 'hermes desktop --build-only' before trying again." >&2
+    return 1
+  fi
+}
+
 # The packaged app can be seeded only beside a runtime at the release it was
-# built from, with its desktop sources untouched, and a seeded app has to be
-# whole. Asked before a command is replaced, so that a refusal leaves the
-# user's Hermes exactly as it was, and again before seeding.
+# built from, with its desktop sources untouched and the Linux runtime patch
+# still able to land. Asked before a command is replaced, so that a refusal
+# leaves the user's Hermes exactly as it was, and again before seeding.
 # Asked through ||, so nothing in here stops on its own: every git answer is
 # checked, and one that cannot be read refuses rather than reading as clean.
 refuse_unless_seedable() {
   local runtime_commit changes
+  refuse_unless_app_whole || return 1
   if [[ -e $native_app || -L $native_app ]]; then
-    if ! native_app_complete; then
-      echo "The Hermes desktop app at $native_app is incomplete. Repair it with 'hermes desktop --build-only' before trying again." >&2
-      return 1
-    fi
     return 0
   fi
   if ! runtime_commit=$(git -C "$runtime" rev-parse HEAD 2>/dev/null) || [[ -z $runtime_commit ]]; then
@@ -399,26 +404,31 @@ refuse_unless_seedable() {
     echo "Hermes desktop sources have local changes. Run 'hermes desktop --build-only', then try again; existing files have been kept." >&2
     return 1
   fi
+  if ! git -C "$runtime" apply --check /usr/share/hermes-desktop/runtime.patch >/dev/null 2>&1 &&
+    ! git -C "$runtime" apply --reverse --check /usr/share/hermes-desktop/runtime.patch >/dev/null 2>&1; then
+    echo "The Hermes Linux runtime patch conflicts with local changes. Existing files have been kept." >&2
+    return 1
+  fi
 }
 
 if [[ $runtime_present == "true" ]]; then
   refuse_unless_seedable || exit 1
+elif [[ -e $runtime || -L $runtime ]]; then
+  # The upstream installer can reset an existing checkout. Do not pin a newer
+  # or modified runtime back to the package release while repairing setup,
+  # and a git state that cannot be read is not a clean one.
+  refuse_unless_app_whole || exit 1
+  if ! runtime_commit=$(git -C "$runtime" rev-parse HEAD 2>/dev/null) || [[ $runtime_commit != "$release_commit" ]] ||
+    ! changes=$(git -C "$runtime" status --porcelain --untracked-files=all 2>/dev/null) || [[ -n $changes ]]; then
+    echo "Hermes setup is incomplete at $runtime. Repair that installation before trying again; existing files have been kept." >&2
+    exit 1
+  fi
 fi
 
 # Whether this run gave Hermes something new to show the theme to: a runtime
 # it set up, or the app it seeded. Putting a command back is neither.
 set_up=false
 
-if [[ $runtime_present == "false" && ( -e $runtime || -L $runtime ) ]]; then
-  # The upstream installer can reset an existing checkout. Do not pin a newer
-  # or modified runtime back to the package release while repairing setup.
-  if [[ $(git -C "$runtime" rev-parse HEAD 2>/dev/null) != "$release_commit" ]] ||
-    [[ -n $(git -C "$runtime" status --porcelain --untracked-files=all) ]]; then
-    echo "Hermes setup is incomplete at $runtime. Repair that installation before trying again; existing files have been kept." >&2
-    exit 1
-  fi
-fi
-
 # The command is the runtime's own and runs; anything else at the path gets
 # replaced below. The retired wrapper is never run to find out.
 command_ready=false