fix: prevent agent deletion from disabling built-ins

Stop delete from creating disable overrides
Delete only the selected agent scope
Keep web and VS Code behavior aligned

packages/web/server/lib/opencode/agents.js

@@ -620,44 +620,68 @@ function updateAgent(agentName, updates, workingDirectory) {
   console.log(`Updated agent: ${agentName} (scope: ${targetScope}, md: ${mdModified}, json: ${jsonModified})`);
 }
 
-function deleteAgent(agentName, workingDirectory) {
-  const lookupCache = createAgentLookupCache();
-  let deleted = false;
+function deleteJsonAgentEntry(config, agentName) {
+  const agentMap = config.agent;
+  if (!agentMap || typeof agentMap !== 'object' || Array.isArray(agentMap) || !agentMap[agentName]) return false;
+  delete agentMap[agentName];
+  if (Object.keys(agentMap).length === 0) {
+    delete config.agent;
+  }
+  return true;
+}
 
-  if (workingDirectory) {
+function deleteAgent(agentName, workingDirectory, scope) {
+  const lookupCache = createAgentLookupCache();
+  const requestedScope = scope === AGENT_SCOPE.PROJECT || scope === AGENT_SCOPE.USER ? scope : null;
+
+  if ((!requestedScope || requestedScope === AGENT_SCOPE.PROJECT) && workingDirectory) {
     const projectPath = getProjectAgentPath(workingDirectory, agentName);
     if (fs.existsSync(projectPath)) {
       fs.unlinkSync(projectPath);
       console.log(`Deleted project-level agent .md file: ${projectPath}`);
-      deleted = true;
+      return;
     }
   }
 
-  const userPath = getUserAgentPath(agentName, lookupCache);
-  if (fs.existsSync(userPath)) {
-    fs.unlinkSync(userPath);
-    console.log(`Deleted user-level agent .md file: ${userPath}`);
-    deleted = true;
+  if (!requestedScope || requestedScope === AGENT_SCOPE.USER) {
+    const userPath = getUserAgentPath(agentName, lookupCache);
+    if (fs.existsSync(userPath)) {
+      fs.unlinkSync(userPath);
+      console.log(`Deleted user-level agent .md file: ${userPath}`);
+      return;
+    }
   }
 
   const layers = readConfigLayers(workingDirectory);
-  const jsonSource = getJsonEntrySource(layers, 'agent', agentName);
-  if (jsonSource.exists && jsonSource.config && jsonSource.path) {
-    if (!jsonSource.config.agent) jsonSource.config.agent = {};
-    delete jsonSource.config.agent[agentName];
-    writeConfig(jsonSource.config, jsonSource.path);
-    console.log(`Removed agent from opencode.json: ${agentName}`);
-    deleted = true;
+
+  if (requestedScope === AGENT_SCOPE.PROJECT) {
+    if (layers.paths.projectPath && deleteJsonAgentEntry(layers.projectConfig, agentName)) {
+      writeConfig(layers.projectConfig, layers.paths.projectPath);
+      console.log(`Removed project-level agent from opencode.json: ${agentName}`);
+      return;
+    }
+    throw new Error(`Project agent ${agentName} not found`);
   }
 
-  if (!deleted) {
-    const jsonTarget = getJsonWriteTarget(layers, workingDirectory ? AGENT_SCOPE.PROJECT : AGENT_SCOPE.USER);
-    const targetConfig = jsonTarget.config || {};
-    if (!targetConfig.agent) targetConfig.agent = {};
-    targetConfig.agent[agentName] = { disable: true };
-    writeConfig(targetConfig, jsonTarget.path || CONFIG_FILE);
-    console.log(`Disabled built-in agent: ${agentName}`);
+  if (requestedScope === AGENT_SCOPE.USER) {
+    const userJsonPath = layers.paths.customPath || layers.paths.userPath;
+    const userJsonConfig = layers.paths.customPath ? layers.customConfig : layers.userConfig;
+    if (userJsonPath && deleteJsonAgentEntry(userJsonConfig, agentName)) {
+      writeConfig(userJsonConfig, userJsonPath);
+      console.log(`Removed user-level agent from opencode.json: ${agentName}`);
+      return;
+    }
+    throw new Error(`User agent ${agentName} not found`);
   }
+
+  const jsonSource = getJsonEntrySource(layers, 'agent', agentName);
+  if (jsonSource.exists && jsonSource.config && jsonSource.path && deleteJsonAgentEntry(jsonSource.config, agentName)) {
+    writeConfig(jsonSource.config, jsonSource.path);
+    console.log(`Removed agent from opencode.json: ${agentName}`);
+    return;
+  }
+
+  throw new Error(`Agent ${agentName} is built-in or not deletable`);
 }
 
 export {

packages/web/server/lib/opencode/config-entity-routes.js

@@ -159,7 +159,8 @@ export const registerConfigEntityRoutes = (app, dependencies) => {
         return res.status(400).json({ error });
       }
 
-      deleteAgent(agentName, directory);
+      const scope = req.body?.scope;
+      deleteAgent(agentName, directory, scope);
       await refreshOpenCodeAfterConfigChange('agent deletion');
 
       res.json({