diff --git a/packages/cli/src/capture.ts b/packages/cli/src/capture.ts
index c9af7e1..ffc1897 100644
--- a/packages/cli/src/capture.ts
+++ b/packages/cli/src/capture.ts
@@ -51,6 +51,7 @@ import {
   getLastDeltaForFile,
 } from "./lib/delta";
 import type { AiAgent } from "./lib/types";
+import { writeHookTrace } from "./lib/hooks";
 
 // =============================================================================
 // Types
@@ -232,6 +233,8 @@ async function setupCaptureContext(
   conversationId: string,
   model: string | null
 ): Promise<CaptureContext | null> {
+  // this will override the config used before we had a payload from the agent. Once we have a payload,
+  // prefer the paths indicated in the payload.
   const repoRoot = await findRepoRoot(filePath);
   if (!repoRoot) {
     if (process.env.AGENTBLAME_DEBUG) {
@@ -819,9 +822,25 @@ export async function runCapture(): Promise<void> {
     }
 
     if (!input.trim()) {
+      console.warn(`[agentblame] Capture: input empty, returning 0`)
       process.exit(0);
     }
 
+    // make best-effort to load an existing config using cwd- payload may override this config dir later in the process
+    const repoRoot = await findRepoRoot(process.cwd());
+    if (!repoRoot) {
+      console.warn(`[agentblame] Capture: could not detect repo root via cwd, configs may not work until we get a payload`)
+    }
+
+    const traceHooks = repoRoot ? await getConfig(repoRoot, 'traceHooks') : false;
+
+    if (traceHooks && repoRoot) {
+      const traceFile = writeHookTrace(repoRoot, input);
+      if (traceFile && process.env.AGENTBLAME_DEBUG) {
+        console.error(`[agentblame] Trace written: ${traceFile}`);
+      }
+    }
+
     const data = JSON.parse(input);
     const payload = data.payload || data;
 
diff --git a/packages/cli/src/index.ts b/packages/cli/src/index.ts
index 3349cc6..3b86c82 100644
--- a/packages/cli/src/index.ts
+++ b/packages/cli/src/index.ts
@@ -252,7 +252,10 @@ async function cleanupGlobalInstall(): Promise<{
 }
 
 async function runInit(initArgs: string[] = []): Promise<void> {
+  // TODO: map these CL switches to config value enum keys
   const forceCleanup = initArgs.includes("--force") || initArgs.includes("-f");
+  const traceHooks = initArgs.includes("--trace-hooks");
+  const storePromptContent = initArgs.includes("--store-prompt-content");
 
   // Check if Bun is installed (required for hooks)
   if (!isBunInstalled()) {
@@ -318,6 +321,11 @@ async function runInit(initArgs: string[] = []): Promise<void> {
     setDatabasePath(dbPath);
     initDatabase();
     results.push({ name: "Database (.git/agentblame/)", success: true });
+    if (traceHooks || storePromptContent) {
+      await setConfig(repoRoot, 'traceHooks', traceHooks);
+      await setConfig(repoRoot, 'storePromptContent', storePromptContent);
+      results.push({ name: `Config values`, success: true });
+    }
   } catch (err) {
     results.push({ name: "Database", success: false });
   }
diff --git a/packages/cli/src/lib/config.ts b/packages/cli/src/lib/config.ts
index d2a8070..ef42b9b 100644
--- a/packages/cli/src/lib/config.ts
+++ b/packages/cli/src/lib/config.ts
@@ -13,10 +13,12 @@ import { runGit } from "./git/gitCli";
 export interface AgentBlameConfig {
   /** Whether to store actual prompt content (default: true) */
   storePromptContent: boolean;
+  traceHooks: boolean;
 }
 
 const CONFIG_DEFAULTS: AgentBlameConfig = {
   storePromptContent: false,  // Default: don't store prompt text (privacy-first)
+  traceHooks: false,          // don't leave debug trace files around unless user opts in
 };
 
 const CONFIG_PREFIX = "agentblame";
diff --git a/packages/cli/src/lib/hooks.ts b/packages/cli/src/lib/hooks.ts
index f699a3c..e98eac0 100644
--- a/packages/cli/src/lib/hooks.ts
+++ b/packages/cli/src/lib/hooks.ts
@@ -786,3 +786,35 @@ export async function uninstallGitHubAction(repoRoot: string): Promise<boolean>
     return false;
   }
 }
+
+
+/**
+ * Write a trace file and log entry
+ * @param agentblameDir - The .agentblame directory
+ * @param input - The raw input string to trace
+ * @returns The trace filename if written, null if tracing disabled
+ */
+export function writeHookTrace(repoRoot: string, input: string): string | null {
+
+  // Create traces directory if needed
+  const agentblameDir = path.join(repoRoot, ".agentblame");
+  const tracesDir = path.join(agentblameDir, "traces");
+  if (!fs.existsSync(tracesDir)) {
+    fs.mkdirSync(tracesDir, { recursive: true });
+  }
+
+  // Generate filename with timestamp
+  const timestamp = new Date().toISOString().replace(/[:.]/g, "-");
+  const filename = `${timestamp}.json`;
+  const tracePath = path.join(tracesDir, filename);
+
+  // Write the trace file
+  fs.writeFileSync(tracePath, input, "utf8");
+
+  // Append to debug.log
+  const logPath = path.join(tracesDir, "traces.log");
+  const logLine = `${new Date().toISOString()} ${filename}\n`;
+  fs.appendFileSync(logPath, logLine, "utf8");
+
+  return filename;
+}