From e322ca68bef8bd0123b36c2b7937c3b1b77a4e2a Mon Sep 17 00:00:00 2001
From: Jarvis <jarvis@woltje.com>
Date: Sat, 20 Jun 2026 16:32:39 -0500
Subject: [PATCH] fix(fleet): preserve agent env overrides on install

---
 packages/mosaic/package.json               |  2 +-
 packages/mosaic/src/commands/fleet.spec.ts | 32 ++++++++++++++++++++++
 packages/mosaic/src/commands/fleet.ts      | 30 +++++++++++++++++---
 3 files changed, 59 insertions(+), 5 deletions(-)

diff --git a/packages/mosaic/package.json b/packages/mosaic/package.json
index b0f9430..540b814 100644
--- a/packages/mosaic/package.json
+++ b/packages/mosaic/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@mosaicstack/mosaic",
-  "version": "0.0.32",
+  "version": "0.0.33",
   "repository": {
     "type": "git",
     "url": "https://git.mosaicstack.dev/mosaicstack/stack.git",
diff --git a/packages/mosaic/src/commands/fleet.spec.ts b/packages/mosaic/src/commands/fleet.spec.ts
index c4ec4c3..28f348b 100644
--- a/packages/mosaic/src/commands/fleet.spec.ts
+++ b/packages/mosaic/src/commands/fleet.spec.ts
@@ -10,6 +10,7 @@ import {
   getDefaultOperatorSourceLabel,
   getRosterAgent,
   loadFleetRoster,
+  mergeAgentEnv,
   registerFleetCommand,
   resolveFleetPaths,
   type CommandRunner,
@@ -121,6 +122,37 @@ describe('fleet roster parsing', () => {
     );
   });
 
+  it('preserves site-owned agent EnvironmentFile overrides while refreshing roster keys', () => {
+    const generated = [
+      'MOSAIC_AGENT_NAME=coder0',
+      'MOSAIC_AGENT_RUNTIME=codex',
+      'MOSAIC_AGENT_WORKDIR=/srv/new',
+      'MOSAIC_TMUX_SOCKET=mosaic-factory',
+      '',
+    ].join('\n');
+    const existing = [
+      'MOSAIC_AGENT_NAME=old-name',
+      'MOSAIC_AGENT_RUNTIME=old-runtime',
+      'MOSAIC_AGENT_WORKDIR=/srv/old',
+      'MOSAIC_TMUX_SOCKET=old-socket',
+      'MOSAIC_AGENT_COMMAND=/home/jarvis/.config/mosaic/fleet/canary.sh',
+      '# site note',
+      '',
+    ].join('\n');
+
+    expect(mergeAgentEnv(generated, existing)).toBe(
+      [
+        'MOSAIC_AGENT_NAME=coder0',
+        'MOSAIC_AGENT_RUNTIME=codex',
+        'MOSAIC_AGENT_WORKDIR=/srv/new',
+        'MOSAIC_TMUX_SOCKET=mosaic-factory',
+        'MOSAIC_AGENT_COMMAND=/home/jarvis/.config/mosaic/fleet/canary.sh',
+        '# site note',
+        '',
+      ].join('\n'),
+    );
+  });
+
   it('rejects unknown roster fields instead of silently defaulting', async () => {
     cleanup = await tempDir();
     const rosterPath = join(cleanup, 'roster.yaml');
diff --git a/packages/mosaic/src/commands/fleet.ts b/packages/mosaic/src/commands/fleet.ts
index 3eb8f61..bcfb85b 100644
--- a/packages/mosaic/src/commands/fleet.ts
+++ b/packages/mosaic/src/commands/fleet.ts
@@ -148,6 +148,29 @@ export function generateAgentEnv(roster: FleetRoster, agent: FleetAgent): string
   ].join('\n');
 }
 
+export function mergeAgentEnv(generatedEnv: string, existingEnv?: string): string {
+  if (!existingEnv?.trim()) {
+    return generatedEnv;
+  }
+  const generatedKeys = new Set(
+    generatedEnv
+      .split('\n')
+      .map((line) => line.match(/^([A-Za-z_][A-Za-z0-9_]*)=/)?.[1])
+      .filter((key): key is string => key !== undefined),
+  );
+  const preservedLines = existingEnv.split('\n').filter((line) => {
+    if (!line.trim()) {
+      return false;
+    }
+    const key = line.match(/^([A-Za-z_][A-Za-z0-9_]*)=/)?.[1];
+    return key === undefined || !generatedKeys.has(key);
+  });
+  if (preservedLines.length === 0) {
+    return generatedEnv;
+  }
+  return [generatedEnv.trimEnd(), ...preservedLines, ''].join('\n');
+}
+
 export function buildFleetServiceCommand(action: FleetServiceAction, agentName?: string): string[] {
   const service = agentName ? `mosaic-agent@${agentName}.service` : 'mosaic-tmux-holder.service';
   return ['systemctl', '--user', action, service];
@@ -477,10 +500,9 @@ async function installFleet(cmd: Command, frameworkRoot: string): Promise<void>
   );
 
   for (const agent of roster.agents) {
-    await writeFile(
-      join(activePaths.agentEnvDir, `${agent.name}.env`),
-      generateAgentEnv(roster, agent),
-    );
+    const envPath = join(activePaths.agentEnvDir, `${agent.name}.env`);
+    const existingEnv = (await canRead(envPath)) ? await readFile(envPath, 'utf8') : undefined;
+    await writeFile(envPath, mergeAgentEnv(generateAgentEnv(roster, agent), existingEnv));
   }
 
   console.log(`Installed fleet files for ${roster.agents.length} agent(s).`);
-- 
2.49.1