diff --git a/agents/gsd-debugger.md b/agents/gsd-debugger.md
index 6f1f4239f..8c7109032 100644
--- a/agents/gsd-debugger.md
+++ b/agents/gsd-debugger.md
@@ -409,6 +409,39 @@ git bisect bad              # or good, based on testing
 
 100 commits between working and broken: ~7 tests to find exact breaking commit.
 
+## Follow the Indirection
+
+**When:** Code constructs paths, URLs, keys, or references from variables — and the constructed value might not point where you expect.
+
+**The trap:** You read code that builds a path like `path.join(configDir, 'hooks')` and assume it's correct because it looks reasonable. But you never verified that the constructed path matches where another part of the system actually writes/reads.
+
+**How:**
+1. Find the code that **produces** the value (writer/installer/creator)
+2. Find the code that **consumes** the value (reader/checker/validator)
+3. Trace the actual resolved value in both — do they agree?
+4. Check every variable in the path construction — where does each come from? What's its actual value at runtime?
+
+**Common indirection bugs:**
+- Path A writes to `dir/sub/hooks/` but Path B checks `dir/hooks/` (directory mismatch)
+- Config value comes from cache/template that wasn't updated
+- Variable is derived differently in two places (e.g., one adds a subdirectory, the other doesn't)
+- Template placeholder (`{{VERSION}}`) not substituted in all code paths
+
+**Example:** Stale hook warning persists after update
+```
+Check code says:  hooksDir = path.join(configDir, 'hooks')
+                  configDir = ~/.claude
+                  → checks ~/.claude/hooks/
+
+Installer says:   hooksDest = path.join(targetDir, 'hooks')
+                  targetDir = ~/.claude/get-shit-done
+                  → writes to ~/.claude/get-shit-done/hooks/
+
+MISMATCH: Checker looks in wrong directory → hooks "not found" → reported as stale
+```
+
+**The discipline:** Never assume a constructed path is correct. Resolve it to its actual value and verify the other side agrees. When two systems share a resource (file, directory, key), trace the full path in both.
+
 ## Technique Selection
 
 | Situation | Technique |
@@ -419,6 +452,7 @@ git bisect bad              # or good, based on testing
 | Know the desired output | Working backwards |
 | Used to work, now doesn't | Differential debugging, Git bisect |
 | Many possible causes | Comment out everything, Binary search |
+| Paths, URLs, keys constructed from variables | Follow the indirection |
 | Always | Observability first (before making changes) |
 
 ## Combining Techniques
diff --git a/bin/install.js b/bin/install.js
index 674120eb4..4f8eeced7 100755
--- a/bin/install.js
+++ b/bin/install.js
@@ -3900,6 +3900,11 @@ function install(isGlobal, runtime = 'claude') {
     }
   }
 
+  // Clear stale update cache so next session re-evaluates hook versions
+  // targetDir is e.g. ~/.claude/get-shit-done/, parent is the config dir
+  const updateCacheFile = path.join(path.dirname(targetDir), 'cache', 'gsd-update-check.json');
+  try { fs.unlinkSync(updateCacheFile); } catch (e) { /* cache may not exist yet */ }
+
   if (failures.length > 0) {
     console.error(`\n  ${yellow}Installation incomplete!${reset} Failed: ${failures.join(', ')}`);
     process.exit(1);
diff --git a/hooks/gsd-check-update.js b/hooks/gsd-check-update.js
index 9076ec038..1b7b27ed3 100755
--- a/hooks/gsd-check-update.js
+++ b/hooks/gsd-check-update.js
@@ -65,9 +65,10 @@ const child = spawn(process.execPath, ['-e', `
   } catch (e) {}
 
   // Check for stale hooks — compare hook version headers against installed VERSION
+  // Hooks live inside get-shit-done/hooks/, not configDir/hooks/
   let staleHooks = [];
   if (configDir) {
-    const hooksDir = path.join(configDir, 'hooks');
+    const hooksDir = path.join(configDir, 'get-shit-done', 'hooks');
     try {
       if (fs.existsSync(hooksDir)) {
         const hookFiles = fs.readdirSync(hooksDir).filter(f => f.startsWith('gsd-') && f.endsWith('.js'));
diff --git a/tests/core.test.cjs b/tests/core.test.cjs
index 68b80c968..2463e30b5 100644
--- a/tests/core.test.cjs
+++ b/tests/core.test.cjs
@@ -968,6 +968,26 @@ describe('stale hook filter', () => {
   });
 });
 
+// ─── stale hook path regression (#1249) ──────────────────────────────────────
+
+describe('stale hook path', () => {
+  test('gsd-check-update.js checks get-shit-done/hooks/ not configDir/hooks/', () => {
+    const content = fs.readFileSync(
+      path.join(__dirname, '..', 'hooks', 'gsd-check-update.js'), 'utf-8'
+    );
+    assert.ok(
+      content.includes("path.join(configDir, 'get-shit-done', 'hooks')"),
+      'stale hook check must look in configDir/get-shit-done/hooks/, not configDir/hooks/'
+    );
+    assert.ok(
+      !content.includes("path.join(configDir, 'hooks')") ||
+      content.indexOf("path.join(configDir, 'get-shit-done', 'hooks')") <
+      content.indexOf("path.join(configDir, 'hooks')") + 100, // allow the old pattern only if corrected version exists first
+      'should not use the wrong hooks path'
+    );
+  });
+});
+
 // ─── resolveWorktreeRoot ─────────────────────────────────────────────────────
 
 describe('resolveWorktreeRoot', () => {