fix: persist agent permission edits

Prevents permission changes from being overwritten by other agent fields
Writes built-in and custom agent permissions to the correct config source
Refreshes agent state after permission saves

packages/ui/src/components/sections/agents/AgentsPage.tsx

@@ -122,6 +122,10 @@ const filterRulesAgainstGlobal = (ruleset: PermissionRule[], globalAction: Permi
 );
 
 const permissionConfigToRuleset = (value: unknown): PermissionRule[] => {
+  if (Array.isArray(value)) {
+    return normalizeRuleset(value as PermissionRule[]);
+  }
+
   if (isPermissionAction(value)) {
     return [{ permission: '*', pattern: '*', action: value }];
   }
@@ -162,9 +166,7 @@ const buildPermissionConfigWithGlobal = (
     (grouped[rule.permission] ||= {})[rule.pattern] = rule.action;
   }
 
-  const result: Record<string, PermissionConfigValue> = {
+  const result: Record<string, PermissionConfigValue> = {};
-    '*': globalAction,
-  };
 
   for (const [permissionName, patterns] of Object.entries(grouped)) {
     if (permissionName === '*') {
@@ -179,6 +181,14 @@ const buildPermissionConfigWithGlobal = (
     result[permissionName] = patterns;
   }
 
+  if (Object.keys(result).length === 0) {
+    return globalAction;
+  }
+
+  if (globalAction !== 'allow') {
+    result['*'] = globalAction;
+  }
+
   return result as AgentConfig['permission'];
 };
 
@@ -273,7 +283,7 @@ export const AgentsPage: React.FC = () => {
     const names = new Set<string>();
 
     for (const agent of agents) {
-      const rules = normalizeRuleset(Array.isArray(agent.permission) ? agent.permission as PermissionRule[] : []);
+      const rules = normalizeRuleset(permissionConfigToRuleset(agent.permission));
       for (const rule of rules) {
         if (rule.permission && rule.permission !== '*' && rule.permission !== 'invalid') {
           names.add(rule.permission);
@@ -509,7 +519,7 @@ export const AgentsPage: React.FC = () => {
       setPrompt(promptValue);
 
       const permissionState = applyPermissionState(
-        Array.isArray(selectedAgent.permission) ? selectedAgent.permission as PermissionRule[] : [],
+        permissionConfigToRuleset(selectedAgent.permission),
       );
 
       initialStateRef.current = {

packages/ui/src/stores/useAgentsStore.ts

@@ -70,12 +70,24 @@ const getAgentsCacheKey = (directory: string | null): string => {
   return directory?.trim() || DEFAULT_AGENTS_CACHE_KEY;
 };
 
+const invalidateAgentsLoadCache = (directory: string | null = getConfigDirectory()) => {
+  agentsLastLoadedAt.delete(getAgentsCacheKey(directory));
+};
+
 const buildAgentsSignature = (agents: Agent[]): string => {
   return agents
     .map((agent) => {
       const extended = agent as AgentWithExtras;
       return [
         agent.name,
+        extended.mode ?? '',
+        typeof extended.model === 'object' && extended.model
+          ? `${extended.model.providerID ?? ''}/${extended.model.modelID ?? ''}`
+          : String(extended.model ?? ''),
+        String(extended.temperature ?? ''),
+        String((extended as { topP?: unknown; top_p?: unknown }).topP ?? (extended as { topP?: unknown; top_p?: unknown }).top_p ?? ''),
+        extended.prompt ?? '',
+        JSON.stringify(extended.permission ?? null),
         extended.scope ?? '',
         extended.group ?? '',
         extended.description ?? '',
@@ -345,6 +357,7 @@ export const useAgentsStore = create<AgentsStore>()(
             }
 
             const needsReload = payload?.requiresReload ?? true;
+            invalidateAgentsLoadCache(configDirectory);
             if (needsReload) {
               requiresReload = true;
               await refreshAfterOpenCodeRestart({
@@ -406,6 +419,7 @@ export const useAgentsStore = create<AgentsStore>()(
             }
 
             const needsReload = payload?.requiresReload ?? true;
+            invalidateAgentsLoadCache(configDirectory);
             if (needsReload) {
               requiresReload = true;
               await refreshAfterOpenCodeRestart({
@@ -452,6 +466,7 @@ export const useAgentsStore = create<AgentsStore>()(
             }
 
             const needsReload = payload?.requiresReload ?? true;
+            invalidateAgentsLoadCache(configDirectory);
             if (needsReload) {
               requiresReload = true;
               await refreshAfterOpenCodeRestart({
@@ -629,6 +644,7 @@ async function performConfigRefresh(options: {
 
     const uiRefreshTasks: Promise<void>[] = [];
     if (refreshAgentConfigs) {
+      invalidateAgentsLoadCache(currentDirectory);
       uiRefreshTasks.push(agentConfigStore.loadAgents().then(() => undefined));
     }
     if (refreshCommands) {

packages/vscode/src/opencodeConfig.ts

@@ -1431,6 +1431,103 @@ const getJsonWriteTarget = (
   return { config: userConfig, path: paths.userPath };
 };
 
+const getAgentPermissionSource = (agentName: string, workingDirectory?: string) => {
+  if (workingDirectory) {
+    const projectMdPath = getProjectAgentPath(workingDirectory, agentName);
+    if (fs.existsSync(projectMdPath)) {
+      const { frontmatter } = parseMdFile(projectMdPath);
+      if (frontmatter.permission !== undefined) {
+        return { source: 'md' as const, scope: AGENT_SCOPE.PROJECT, path: projectMdPath };
+      }
+    }
+  }
+
+  const userMdPath = getUserAgentPath(agentName);
+  if (fs.existsSync(userMdPath)) {
+    const { frontmatter } = parseMdFile(userMdPath);
+    if (frontmatter.permission !== undefined) {
+      return { source: 'md' as const, scope: AGENT_SCOPE.USER, path: userMdPath };
+    }
+  }
+
+  const layers = readConfigLayers(workingDirectory);
+  const customAgent = ((layers.customConfig as Record<string, unknown>)?.agent as Record<string, unknown> | undefined)?.[agentName] as Record<string, unknown> | undefined;
+  if (customAgent?.permission !== undefined && layers.paths.customPath) {
+    return { source: 'json' as const, scope: 'custom' as const, path: layers.paths.customPath };
+  }
+
+  const projectAgent = ((layers.projectConfig as Record<string, unknown>)?.agent as Record<string, unknown> | undefined)?.[agentName] as Record<string, unknown> | undefined;
+  if (projectAgent?.permission !== undefined && layers.paths.projectPath) {
+    return { source: 'json' as const, scope: AGENT_SCOPE.PROJECT, path: layers.paths.projectPath };
+  }
+
+  const userAgent = ((layers.userConfig as Record<string, unknown>)?.agent as Record<string, unknown> | undefined)?.[agentName] as Record<string, unknown> | undefined;
+  if (userAgent?.permission !== undefined) {
+    return { source: 'json' as const, scope: AGENT_SCOPE.USER, path: layers.paths.userPath };
+  }
+
+  return { source: null, scope: null, path: null };
+};
+
+const mergePermissionWithNonWildcards = (newPermission: unknown, permissionSource: ReturnType<typeof getAgentPermissionSource>, agentName: string) => {
+  if (!permissionSource.source || !permissionSource.path) {
+    return newPermission;
+  }
+
+  let existingPermission: unknown = null;
+  if (permissionSource.source === 'md') {
+    const { frontmatter } = parseMdFile(permissionSource.path);
+    existingPermission = frontmatter.permission;
+  } else if (permissionSource.source === 'json') {
+    const config = readConfigFile(permissionSource.path) as Record<string, unknown>;
+    existingPermission = (((config.agent as Record<string, unknown> | undefined)?.[agentName] as Record<string, unknown> | undefined)?.permission);
+  }
+
+  if (!existingPermission || typeof existingPermission === 'string' || newPermission == null || typeof newPermission === 'string') {
+    return newPermission;
+  }
+
+  if (typeof existingPermission !== 'object' || Array.isArray(existingPermission) || typeof newPermission !== 'object' || Array.isArray(newPermission)) {
+    return newPermission;
+  }
+
+  const nonWildcardPatterns: Record<string, Record<string, unknown>> = {};
+  for (const [permKey, permValue] of Object.entries(existingPermission as Record<string, unknown>)) {
+    if (permKey === '*' || typeof permValue !== 'object' || permValue === null || Array.isArray(permValue)) continue;
+    const nonWildcards: Record<string, unknown> = {};
+    for (const [pattern, action] of Object.entries(permValue as Record<string, unknown>)) {
+      if (pattern !== '*') {
+        nonWildcards[pattern] = action;
+      }
+    }
+    if (Object.keys(nonWildcards).length > 0) {
+      nonWildcardPatterns[permKey] = nonWildcards;
+    }
+  }
+
+  if (Object.keys(nonWildcardPatterns).length === 0) {
+    return newPermission;
+  }
+
+  const merged: Record<string, unknown> = { ...(newPermission as Record<string, unknown>) };
+  for (const [permKey, patterns] of Object.entries(nonWildcardPatterns)) {
+    const newValue = merged[permKey];
+    if (typeof newValue === 'string') {
+      merged[permKey] = { '*': newValue, ...patterns };
+    } else if (typeof newValue === 'object' && newValue !== null && !Array.isArray(newValue)) {
+      merged[permKey] = { ...patterns, ...(newValue as Record<string, unknown>) };
+    } else {
+      const existingValue = (existingPermission as Record<string, unknown>)[permKey];
+      if (typeof existingValue === 'object' && existingValue !== null && !Array.isArray(existingValue)) {
+        const wildcard = (existingValue as Record<string, unknown>)['*'];
+        merged[permKey] = wildcard ? { '*': wildcard, ...patterns } : patterns;
+      }
+    }
+  }
+
+  return merged;
+};
+
 const parseMdFile = (filePath: string): { frontmatter: Record<string, unknown>; body: string } => {
   const content = fs.readFileSync(filePath, 'utf8');
   const match = content.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n([\s\S]*)$/);
@@ -1545,7 +1642,7 @@ export const updateAgent = (agentName: string, updates: Record<string, unknown>,
   const hasJsonFields = Boolean(jsonSource.exists && jsonSection && Object.keys(jsonSection).length > 0);
   const jsonTarget = jsonSource.exists
     ? { config: jsonSource.config, path: jsonSource.path }
-    : getJsonWriteTarget(layers, workingDirectory ? AGENT_SCOPE.PROJECT : AGENT_SCOPE.USER);
+    : getJsonWriteTarget(layers, AGENT_SCOPE.USER);
   const config = (jsonTarget.config || {}) as Record<string, unknown>;
   
   // Determine if we should create a new md file:
@@ -1594,6 +1691,53 @@ export const updateAgent = (agentName: string, updates: Record<string, unknown>,
       continue;
     }
 
+    if (field === 'permission') {
+      const permissionSource = getAgentPermissionSource(agentName, workingDirectory);
+      const newPermission = mergePermissionWithNonWildcards(value, permissionSource, agentName);
+
+      if (permissionSource.source === 'md' && permissionSource.path) {
+        if (mdData && permissionSource.path === targetPath) {
+          mdData.frontmatter.permission = newPermission;
+          mdModified = true;
+        } else {
+          const existingMdData = parseMdFile(permissionSource.path);
+          existingMdData.frontmatter.permission = newPermission;
+          writeMdFile(permissionSource.path, existingMdData.frontmatter, existingMdData.body);
+        }
+      } else if (permissionSource.source === 'json' && permissionSource.path) {
+        if (permissionSource.path === (jsonTarget.path || CONFIG_FILE)) {
+          if (!config.agent) config.agent = {};
+          const current = ((config.agent as Record<string, unknown>)[agentName] as Record<string, unknown> | undefined) ?? {};
+          (config.agent as Record<string, unknown>)[agentName] = { ...current, permission: newPermission };
+          jsonModified = true;
+        } else {
+          const existingConfig = readConfigFile(permissionSource.path) as Record<string, unknown>;
+          const agentMap = (existingConfig.agent as Record<string, unknown> | undefined) ?? {};
+          const current = (agentMap[agentName] as Record<string, unknown> | undefined) ?? {};
+          agentMap[agentName] = { ...current, permission: newPermission };
+          existingConfig.agent = agentMap;
+          writeConfig(existingConfig, permissionSource.path);
+        }
+      } else if (mdExists && mdData) {
+        mdData.frontmatter.permission = newPermission;
+        mdModified = true;
+      } else if (hasJsonFields) {
+        if (!config.agent) config.agent = {};
+        const current = ((config.agent as Record<string, unknown>)[agentName] as Record<string, unknown> | undefined) ?? {};
+        (config.agent as Record<string, unknown>)[agentName] = { ...current, permission: newPermission };
+        jsonModified = true;
+      } else {
+        const writeTarget = getJsonWriteTarget(layers, AGENT_SCOPE.USER);
+        const targetConfig = (writeTarget.config || {}) as Record<string, unknown>;
+        const agentMap = (targetConfig.agent as Record<string, unknown> | undefined) ?? {};
+        const current = (agentMap[agentName] as Record<string, unknown> | undefined) ?? {};
+        agentMap[agentName] = { ...current, permission: newPermission };
+        targetConfig.agent = agentMap;
+        writeConfig(targetConfig, writeTarget.path || CONFIG_FILE);
+      }
+      continue;
+    }
+
     const hasMdField = Boolean(mdData?.frontmatter?.[field] !== undefined);
     const hasJsonField = Boolean(jsonSection?.[field] !== undefined);
 

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

@@ -193,27 +193,25 @@ function getAgentPermissionSource(agentName, workingDirectory, lookupCache = nul
     }
   }
 
-  // Check JSON layers (project > user)
+  // Check JSON layers in effective override order. readConfigLayers merges
+  // user -> project -> custom, so custom wins over project, project over user.
   const layers = readConfigLayers(workingDirectory);
 
-  // Project opencode.json
+  const customJsonPermission = layers.customConfig?.agent?.[agentName]?.permission;
+  if (customJsonPermission !== undefined && layers.paths.customPath) {
+    return { source: 'json', scope: 'custom', path: layers.paths.customPath };
+  }
+
   const projectJsonPermission = layers.projectConfig?.agent?.[agentName]?.permission;
   if (projectJsonPermission !== undefined && layers.paths.projectPath) {
     return { source: 'json', scope: AGENT_SCOPE.PROJECT, path: layers.paths.projectPath };
   }
 
-  // User opencode.json
   const userJsonPermission = layers.userConfig?.agent?.[agentName]?.permission;
   if (userJsonPermission !== undefined) {
     return { source: 'json', scope: AGENT_SCOPE.USER, path: layers.paths.userPath };
   }
 
-  // Custom config (env var)
-  const customJsonPermission = layers.customConfig?.agent?.[agentName]?.permission;
-  if (customJsonPermission !== undefined && layers.paths.customPath) {
-    return { source: 'json', scope: 'custom', path: layers.paths.customPath };
-  }
-
   return { source: null, scope: null, path: null };
 }
 
@@ -486,19 +484,31 @@ function updateAgent(agentName, updates, workingDirectory) {
       const newPermission = mergePermissionWithNonWildcards(value, permissionSource, agentName);
 
       if (permissionSource.source === 'md') {
-        const existingMdData = parseMdFile(permissionSource.path);
+        if (mdData && permissionSource.path === targetPath) {
-        existingMdData.frontmatter.permission = newPermission;
+          mdData.frontmatter.permission = newPermission;
-        writeMdFile(permissionSource.path, existingMdData.frontmatter, existingMdData.body);
+          mdModified = true;
-        console.log(`Updated permission in .md file: ${permissionSource.path}`);
+        } else {
+          const existingMdData = parseMdFile(permissionSource.path);
+          existingMdData.frontmatter.permission = newPermission;
+          writeMdFile(permissionSource.path, existingMdData.frontmatter, existingMdData.body);
+          console.log(`Updated permission in .md file: ${permissionSource.path}`);
+        }
       } else if (permissionSource.source === 'json') {
-        const existingConfig = readConfigFile(permissionSource.path);
+        if (permissionSource.path === (jsonTarget.path || CONFIG_FILE)) {
-        if (!existingConfig.agent) existingConfig.agent = {};
+          if (!config.agent) config.agent = {};
-        if (!existingConfig.agent[agentName]) existingConfig.agent[agentName] = {};
+          if (!config.agent[agentName]) config.agent[agentName] = {};
-        existingConfig.agent[agentName].permission = newPermission;
+          config.agent[agentName].permission = newPermission;
-        writeConfig(existingConfig, permissionSource.path);
+          jsonModified = true;
-        console.log(`Updated permission in JSON: ${permissionSource.path}`);
+        } else {
+          const existingConfig = readConfigFile(permissionSource.path);
+          if (!existingConfig.agent) existingConfig.agent = {};
+          if (!existingConfig.agent[agentName]) existingConfig.agent[agentName] = {};
+          existingConfig.agent[agentName].permission = newPermission;
+          writeConfig(existingConfig, permissionSource.path);
+          console.log(`Updated permission in JSON: ${permissionSource.path}`);
+        }
       } else {
-        if ((mdExists || creatingNewMd) && mdData) {
+        if (mdExists && mdData) {
           mdData.frontmatter.permission = newPermission;
           mdModified = true;
         } else if (hasJsonFields) {
@@ -507,9 +517,7 @@ function updateAgent(agentName, updates, workingDirectory) {
           config.agent[agentName].permission = newPermission;
           jsonModified = true;
         } else {
-          const writeTarget = workingDirectory
+          const writeTarget = getJsonWriteTarget(layers, AGENT_SCOPE.USER);
-            ? { config: layers.projectConfig || {}, path: layers.paths.projectPath || layers.paths.userPath }
-            : { config: layers.userConfig || {}, path: layers.paths.userPath };
           if (!writeTarget.config.agent) writeTarget.config.agent = {};
           if (!writeTarget.config.agent[agentName]) writeTarget.config.agent[agentName] = {};
           writeTarget.config.agent[agentName].permission = newPermission;