Add setting_sources input and default base-action to user-only

action.yml

@@ -62,6 +62,10 @@ inputs:
     description: "Claude Code settings as JSON string or path to settings JSON file"
     required: false
     default: ""
+  setting_sources:
+    description: "Comma-separated list of setting sources to load (user, project, local). Defaults to 'user,project,local' — project settings are safe here because .claude/ is restored from the PR base branch before execution. Set to 'user' to ignore in-repo settings entirely."
+    required: false
+    default: "user,project,local"
 
   # Auth configuration
   anthropic_api_key:
@@ -233,6 +237,7 @@ runs:
         # Base-action inputs
         INPUT_PROMPT_FILE: ${{ runner.temp }}/claude-prompts/claude-prompt.txt
         INPUT_SETTINGS: ${{ inputs.settings }}
+        INPUT_SETTING_SOURCES: ${{ inputs.setting_sources }}
         INPUT_EXPERIMENTAL_SLASH_COMMANDS_DIR: ${{ github.action_path }}/slash-commands
         INPUT_PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
         INPUT_PATH_TO_BUN_EXECUTABLE: ${{ inputs.path_to_bun_executable }}

base-action/README.md

@@ -94,6 +94,7 @@ Add the following to your workflow file:
 | `max_turns`               | Maximum number of conversation turns (default: no limit)                                                                | No       | ''                           |
 | `mcp_config`              | Path to the MCP configuration JSON file, or MCP configuration JSON string                                               | No       | ''                           |
 | `settings`                | Path to Claude Code settings JSON file, or settings JSON string                                                         | No       | ''                           |
+| `setting_sources`         | Comma-separated setting sources to load (`user`, `project`, `local`). Project/local merge permissions additively.       | No       | 'user'                       |
 | `system_prompt`           | Override system prompt                                                                                                  | No       | ''                           |
 | `append_system_prompt`    | Append to system prompt                                                                                                 | No       | ''                           |
 | `claude_env`              | Custom environment variables to pass to Claude Code execution (YAML multiline format)                                   | No       | ''                           |

base-action/action.yml

@@ -18,6 +18,10 @@ inputs:
     description: "Claude Code settings as JSON string or path to settings JSON file"
     required: false
     default: ""
+  setting_sources:
+    description: "Comma-separated list of setting sources to load (user, project, local). Defaults to 'user' only. Project/local settings additively merge permissions with allowed_tools — set to 'user,project,local' to opt in."
+    required: false
+    default: ""
 
   # Action settings
   claude_args:
@@ -165,6 +169,7 @@ runs:
         INPUT_PROMPT: ${{ inputs.prompt }}
         INPUT_PROMPT_FILE: ${{ inputs.prompt_file }}
         INPUT_SETTINGS: ${{ inputs.settings }}
+        INPUT_SETTING_SOURCES: ${{ inputs.setting_sources }}
         INPUT_CLAUDE_ARGS: ${{ inputs.claude_args }}
         INPUT_PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
         INPUT_PATH_TO_BUN_EXECUTABLE: ${{ inputs.path_to_bun_executable }}

base-action/src/index.ts

@@ -41,6 +41,7 @@ async function run() {
       pathToClaudeCodeExecutable:
         process.env.INPUT_PATH_TO_CLAUDE_CODE_EXECUTABLE,
       showFullOutput: process.env.INPUT_SHOW_FULL_OUTPUT,
+      settingSources: process.env.INPUT_SETTING_SOURCES,
     });
 
     // Set outputs for the standalone base-action

base-action/src/parse-sdk-options.ts

@@ -251,13 +251,15 @@ export function parseSdkOptions(options: ClaudeOptions): ParsedSdkOptions {
     extraArgs,
     env,
 
-    // Load settings from sources - prefer user's --setting-sources if provided, otherwise use all sources
-    // This ensures users can override the default behavior (e.g., --setting-sources user to avoid in-repo configs)
-    settingSources: extraArgs["setting-sources"]
-      ? (extraArgs["setting-sources"].split(
-          ",",
-        ) as SdkOptions["settingSources"])
-      : ["user", "project", "local"],
+    // Setting sources precedence: direct input > --setting-sources in claude_args > default.
+    // Default is ["user"] only: project/local settings additively merge permissions with
+    // allowedTools, which silently expands a workflow's intended allow-set. Workflows that
+    // want project settings must opt in explicitly.
+    settingSources: (options.settingSources
+      ? options.settingSources.split(",").map((s) => s.trim())
+      : extraArgs["setting-sources"]
+        ? extraArgs["setting-sources"].split(",").map((s) => s.trim())
+        : ["user"]) as SdkOptions["settingSources"],
   };
 
   // Remove setting-sources from extraArgs to avoid passing it twice

base-action/src/run-claude.ts

@@ -14,6 +14,7 @@ export type ClaudeOptions = {
   appendSystemPrompt?: string;
   fallbackModel?: string;
   showFullOutput?: string;
+  settingSources?: string;
 };
 
 export async function runClaude(

base-action/test/parse-sdk-options.test.ts

@@ -367,4 +367,59 @@ describe("parseSdkOptions", () => {
       );
     });
   });
+
+  describe("settingSources", () => {
+    test("should default to ['user'] when not specified", () => {
+      const options: ClaudeOptions = {};
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.settingSources).toEqual(["user"]);
+    });
+
+    test("should use direct settingSources input when provided", () => {
+      const options: ClaudeOptions = {
+        settingSources: "user,project,local",
+      };
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.settingSources).toEqual([
+        "user",
+        "project",
+        "local",
+      ]);
+    });
+
+    test("should use --setting-sources from claudeArgs when no direct input", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: "--setting-sources user,project",
+      };
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.settingSources).toEqual(["user", "project"]);
+      expect(result.sdkOptions.extraArgs?.["setting-sources"]).toBeUndefined();
+    });
+
+    test("direct input should take precedence over claudeArgs", () => {
+      const options: ClaudeOptions = {
+        settingSources: "user",
+        claudeArgs: "--setting-sources user,project,local",
+      };
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.settingSources).toEqual(["user"]);
+    });
+
+    test("should trim whitespace in comma-separated values", () => {
+      const options: ClaudeOptions = {
+        settingSources: "user, project , local",
+      };
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.settingSources).toEqual([
+        "user",
+        "project",
+        "local",
+      ]);
+    });
+  });
 });

src/entrypoints/run.ts

@@ -272,6 +272,7 @@ async function run() {
       pathToClaudeCodeExecutable:
         process.env.INPUT_PATH_TO_CLAUDE_CODE_EXECUTABLE,
       showFullOutput: process.env.INPUT_SHOW_FULL_OUTPUT,
+      settingSources: process.env.INPUT_SETTING_SOURCES,
     });
 
     claudeSuccess = claudeResult.conclusion === "success";