refactor(signals): restructure signal handling and consolidate directives

move signal handling logic from directives to new signals module
add signal manager to centralize event listeners and context
update runner to use signal manager instead of directive manager
move skip logic from directives to step/skip.ts
update imports and references across the codebase

Author: moazbuilds

src/cli/tui/app-shell.tsx

@@ -196,7 +196,7 @@ export function App(props: { initialToast?: InitialToast }) {
     const specPath = path.join(cwd, '.codemachine', 'inputs', 'specifications.md')
 
     pendingWorkflowStart = () => {
-      import("../../workflows/execution/run.js").then(({ runWorkflow }) => {
+      import("../../workflows/run.js").then(({ runWorkflow }) => {
         runWorkflow({ cwd, specificationPath: specPath }).catch((error) => {
           // Emit error event to show toast with actual error message
           const errorMsg = error instanceof Error ? error.message : String(error)

src/cli/tui/routes/home/hooks/use-home-commands.tsx

@@ -63,7 +63,7 @@ export function useHomeCommands(options: UseHomeCommandsOptions) {
     const specPath = getAbsoluteSpecPath()
 
     try {
-      const { validateSpecification } = await import("../../../../../workflows/execution/run.js")
+      const { validateSpecification } = await import("../../../../../workflows/run.js")
       await validateSpecification(specPath)
     } catch (error) {
       if (error instanceof Error) {

src/workflows/directives/index.ts

@@ -3,14 +3,22 @@
  *
  * Agent-issued instructions that control workflow execution.
  * Agents write to directive.json to issue directives.
+ *
+ * Supported directives:
+ * - loop: Repeat steps
+ * - checkpoint: Pause for user confirmation
+ * - trigger: Execute another agent
+ * - error: Report workflow error
+ * - pause: Agent requests pause (different from user keypress)
+ *
+ * Note: skip logic moved to step/skip.ts
+ * Note: signal manager moved to signals/manager
  */
 
 export * from './types.js';
 export * from './reader.js';
-export * from './skip.js';
 export * from './loop/index.js';
 export * from './trigger/index.js';
 export * from './checkpoint/index.js';
 export * from './error/index.js';
-export * from './manager/index.js';
 export * from './pause/index.js';