feat: mount user repo as read-only with writable shannon overlay (#273)

* feat: mount user repo as read-only with deliverables bind-mount overlay

* feat: add playground and .playwright-cli overlay mounts

* feat: add filesystem context to pipeline-testing prompts

* fix: use explicit REPO_PATH in filesystem prompt for clarity

* fix: update filesystem prompts with playground notes and absolute screenshot paths

* feat: namespace writable overlays under .shannon/ to avoid polluting host repo

* refactor: rename playground to scratchpad

* fix: redirect playwright-cli output to writable .shannon/ overlay

* fix: pre-create .shannon/ overlay mount points for Linux compatibility

* fix: exclude nested node_modules and dist from Docker build context

* fix: enforce LF line endings for shell scripts on Windows

apps/worker/src/services/agent-execution.ts

@@ -44,6 +44,7 @@ import { loadPrompt } from './prompt-manager.js';
 export interface AgentExecutionInput {
   webUrl: string;
   repoPath: string;
+  deliverablesPath: string;
   configPath?: string | undefined;
   pipelineTestingMode?: boolean | undefined;
   attemptNumber: number;
@@ -89,7 +90,7 @@ export class AgentExecutionService {
     auditSession: AuditSession,
     logger: ActivityLogger,
   ): Promise<Result<AgentEndResult, PentestError>> {
-    const { webUrl, repoPath, configPath, pipelineTestingMode = false, attemptNumber } = input;
+    const { webUrl, repoPath, deliverablesPath, configPath, pipelineTestingMode = false, attemptNumber } = input;
 
     // 1. Load config (if provided)
     const configResult = await this.configLoader.loadOptional(configPath);
@@ -118,7 +119,7 @@ export class AgentExecutionService {
 
     // 3. Create git checkpoint before execution
     try {
-      await createGitCheckpoint(repoPath, agentName, attemptNumber, logger);
+      await createGitCheckpoint(deliverablesPath, agentName, attemptNumber, logger);
     } catch (error) {
       const errorMessage = error instanceof Error ? error.message : String(error);
       return err(
@@ -126,7 +127,7 @@ export class AgentExecutionService {
           `Failed to create git checkpoint for ${agentName}: ${errorMessage}`,
           'filesystem',
           false,
-          { agentName, repoPath, originalError: errorMessage },
+          { agentName, deliverablesPath, originalError: errorMessage },
           ErrorCode.GIT_CHECKPOINT_FAILED,
         ),
       );
@@ -153,7 +154,7 @@ export class AgentExecutionService {
     if (result.success && (result.turns ?? 0) <= 2 && (result.cost || 0) === 0) {
       const resultText = result.result || '';
       if (isSpendingCapBehavior(result.turns ?? 0, result.cost || 0, resultText)) {
-        return this.failAgent(agentName, repoPath, auditSession, logger, {
+        return this.failAgent(agentName, deliverablesPath, auditSession, logger, {
           attemptNumber,
           result,
           rollbackReason: 'spending cap detected',
@@ -168,7 +169,7 @@ export class AgentExecutionService {
 
     // 7. Handle execution failure
     if (!result.success) {
-      return this.failAgent(agentName, repoPath, auditSession, logger, {
+      return this.failAgent(agentName, deliverablesPath, auditSession, logger, {
         attemptNumber,
         result,
         rollbackReason: 'execution failure',
@@ -183,7 +184,7 @@ export class AgentExecutionService {
     // 8. Write structured output to disk (vuln agents only)
     const queueFilename = getQueueFilename(agentName);
     if (result.structuredOutput !== undefined && queueFilename) {
-      const deliverablesDir = path.join(repoPath, 'deliverables');
+      const deliverablesDir = path.join(repoPath, '.shannon', 'deliverables');
       await fs.ensureDir(deliverablesDir);
       const queuePath = path.join(deliverablesDir, queueFilename);
       await fs.writeFile(queuePath, JSON.stringify(result.structuredOutput, null, 2), 'utf8');
@@ -193,7 +194,7 @@ export class AgentExecutionService {
     // 9. Validate output
     const validationPassed = await validateAgentOutput(result, agentName, repoPath, logger);
     if (!validationPassed) {
-      return this.failAgent(agentName, repoPath, auditSession, logger, {
+      return this.failAgent(agentName, deliverablesPath, auditSession, logger, {
         attemptNumber,
         result,
         rollbackReason: 'validation failure',
@@ -206,8 +207,8 @@ export class AgentExecutionService {
     }
 
     // 10. Success - commit deliverables, then capture checkpoint hash
-    await commitGitSuccess(repoPath, agentName, logger);
-    const commitHash = await getGitCommitHash(repoPath);
+    await commitGitSuccess(deliverablesPath, agentName, logger);
+    const commitHash = await getGitCommitHash(deliverablesPath);
 
     const endResult: AgentEndResult = {
       attemptNumber,
@@ -224,12 +225,12 @@ export class AgentExecutionService {
 
   private async failAgent(
     agentName: AgentName,
-    repoPath: string,
+    deliverablesPath: string,
     auditSession: AuditSession,
     logger: ActivityLogger,
     opts: FailAgentOpts,
   ): Promise<Result<AgentEndResult, PentestError>> {
-    await rollbackGitWorkspace(repoPath, opts.rollbackReason, logger);
+    await rollbackGitWorkspace(deliverablesPath, opts.rollbackReason, logger);
 
     const endResult: AgentEndResult = {
       attemptNumber: opts.attemptNumber,

apps/worker/src/services/queue-validation.ts

@@ -133,8 +133,8 @@ const createPaths = (vulnType: VulnType, sourceDir: string): PathsBase | PathsWi
 
   return Object.freeze({
     vulnType,
-    deliverable: path.join(sourceDir, 'deliverables', config.deliverable),
-    queue: path.join(sourceDir, 'deliverables', config.queue),
+    deliverable: path.join(sourceDir, '.shannon', 'deliverables', config.deliverable),
+    queue: path.join(sourceDir, '.shannon', 'deliverables', config.queue),
     sourceDir,
   });
 };

apps/worker/src/services/reporting.ts

@@ -28,7 +28,7 @@ export async function assembleFinalReport(sourceDir: string, logger: ActivityLog
   const sections: string[] = [];
 
   for (const file of deliverableFiles) {
-    const filePath = path.join(sourceDir, 'deliverables', file.path);
+    const filePath = path.join(sourceDir, '.shannon', 'deliverables', file.path);
     try {
       if (await fs.pathExists(filePath)) {
         const content = await fs.readFile(filePath, 'utf8');
@@ -55,7 +55,7 @@ export async function assembleFinalReport(sourceDir: string, logger: ActivityLog
   }
 
   const finalContent = sections.join('\n\n');
-  const deliverablesDir = path.join(sourceDir, 'deliverables');
+  const deliverablesDir = path.join(sourceDir, '.shannon', 'deliverables');
   const finalReportPath = path.join(deliverablesDir, 'comprehensive_security_assessment_report.md');
 
   try {
@@ -117,7 +117,7 @@ export async function injectModelIntoReport(
   logger.info(`Injecting model info into report: ${modelStr}`);
 
   // 3. Read the final report
-  const reportPath = path.join(repoPath, 'deliverables', 'comprehensive_security_assessment_report.md');
+  const reportPath = path.join(repoPath, '.shannon', 'deliverables', 'comprehensive_security_assessment_report.md');
 
   if (!(await fs.pathExists(reportPath))) {
     logger.warn('Final report not found, skipping model injection');