diff --git a/CLAUDE.md b/CLAUDE.md
index 9e429d8..23cf432 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -92,7 +92,7 @@ qmd context rm /  # Remove global context
 ## Development
 
 ```sh
-bun qmd.ts <command>   # Run from source
+bun src/qmd.ts <command>   # Run from source
 bun link               # Install globally as 'qmd'
 ```
 
@@ -113,4 +113,4 @@ bun link               # Install globally as 'qmd'
 ## Do NOT compile
 
 - Never run `bun build --compile` - it overwrites the shell wrapper and breaks sqlite-vec
-- The `qmd` file is a shell script that runs `bun qmd.ts` - do not replace it
\ No newline at end of file
+- The `qmd` file is a shell script that runs `bun src/qmd.ts` - do not replace it
\ No newline at end of file
diff --git a/README.md b/README.md
index 2424265..8bea647 100644
--- a/README.md
+++ b/README.md
@@ -466,7 +466,7 @@ Query ──► LLM Expansion ──► [Original, Variant 1, Variant 2]
 
 ## Model Configuration
 
-Models are configured as constants in `qmd.ts`:
+Models are configured as constants in `src/qmd.ts`:
 
 ```typescript
 const DEFAULT_EMBED_MODEL = "embeddinggemma";
diff --git a/package.json b/package.json
index 18c52de..d3dd836 100644
--- a/package.json
+++ b/package.json
@@ -8,14 +8,14 @@
   },
   "scripts": {
     "test": "bun test",
-    "qmd": "bun qmd.ts",
-    "index": "bun qmd.ts index",
-    "vector": "bun qmd.ts vector",
-    "search": "bun qmd.ts search",
-    "vsearch": "bun qmd.ts vsearch",
-    "rerank": "bun qmd.ts rerank",
+    "qmd": "bun src/qmd.ts",
+    "index": "bun src/qmd.ts index",
+    "vector": "bun src/qmd.ts vector",
+    "search": "bun src/qmd.ts search",
+    "vsearch": "bun src/qmd.ts vsearch",
+    "rerank": "bun src/qmd.ts rerank",
     "link": "bun link",
-    "inspector": "npx @modelcontextprotocol/inspector bun qmd.ts mcp"
+    "inspector": "npx @modelcontextprotocol/inspector bun src/qmd.ts mcp"
   },
   "dependencies": {
     "@modelcontextprotocol/sdk": "^1.24.3",
diff --git a/qmd b/qmd
index 7db8a3c..3281acb 100755
--- a/qmd
+++ b/qmd
@@ -11,4 +11,4 @@ while [ -L "$SOURCE" ]; do
 done
 SCRIPT_DIR="$(cd -P "$(dirname "$SOURCE")" && pwd)"
 
-exec bun "$SCRIPT_DIR/qmd.ts" "$@"
+exec bun "$SCRIPT_DIR/src/qmd.ts" "$@"
diff --git a/cli.test.ts b/src/cli.test.ts
similarity index 100%
rename from cli.test.ts
rename to src/cli.test.ts
diff --git a/context-ops.ts b/src/context-ops.ts
similarity index 100%
rename from context-ops.ts
rename to src/context-ops.ts
diff --git a/formatter.ts b/src/formatter.ts
similarity index 100%
rename from formatter.ts
rename to src/formatter.ts
diff --git a/llm.test.ts b/src/llm.test.ts
similarity index 100%
rename from llm.test.ts
rename to src/llm.test.ts
diff --git a/llm.ts b/src/llm.ts
similarity index 100%
rename from llm.ts
rename to src/llm.ts
diff --git a/mcp.test.ts b/src/mcp.test.ts
similarity index 100%
rename from mcp.test.ts
rename to src/mcp.test.ts
diff --git a/mcp.ts b/src/mcp.ts
similarity index 100%
rename from mcp.ts
rename to src/mcp.ts
diff --git a/qmd.ts b/src/qmd.ts
similarity index 97%
rename from qmd.ts
rename to src/qmd.ts
index 46976b7..a24cbbc 100755
--- a/qmd.ts
+++ b/src/qmd.ts
@@ -512,7 +512,7 @@ function showStatus(): void {
   closeDb();
 }
 
-async function updateCollections(): Promise<void> {
+async function updateCollections(pullFirst: boolean = false): Promise<void> {
   const db = getDb();
   cleanupDuplicateCollections(db);
 
@@ -534,6 +534,59 @@ async function updateCollections(): Promise<void> {
     const col = collections[i];
     console.log(`${c.cyan}[${i + 1}/${collections.length}]${c.reset} ${c.bold}${col.pwd}${c.reset}`);
     console.log(`${c.dim}    Pattern: ${col.glob_pattern}${c.reset}`);
+
+    // Check if this is a git repository
+    const gitDir = `${col.pwd}/.git`;
+    let isGitRepo = false;
+
+    try {
+      const stat = await Bun.file(gitDir).exists();
+      isGitRepo = stat;
+    } catch {
+      // Not a git repo or can't access
+      isGitRepo = false;
+    }
+
+    if (isGitRepo) {
+      console.log(`${c.dim}    Git repository detected${c.reset}`);
+
+      // Execute git pull if requested
+      if (pullFirst) {
+        console.log(`${c.dim}    Running git pull...${c.reset}`);
+        try {
+          const result = await $`cd ${col.pwd} && git pull`.quiet();
+          if (result.exitCode === 0) {
+            const output = result.stdout.toString().trim();
+            if (output) {
+              // Show output but dimmed
+              console.log(`${c.dim}    ${output.split('\n').join('\n    ')}${c.reset}`);
+            }
+          } else {
+            const stderr = result.stderr.toString().trim();
+            console.log(`${c.yellow}    Warning: git pull failed: ${stderr}${c.reset}`);
+          }
+        } catch (err) {
+          console.log(`${c.yellow}    Warning: git pull failed: ${err}${c.reset}`);
+        }
+      }
+
+      // Show git status
+      try {
+        const statusResult = await $`cd ${col.pwd} && git status --short`.quiet();
+        if (statusResult.exitCode === 0) {
+          const statusOutput = statusResult.stdout.toString().trim();
+          if (statusOutput) {
+            console.log(`${c.dim}    Git status:${c.reset}`);
+            console.log(`${c.dim}    ${statusOutput.split('\n').join('\n    ')}${c.reset}`);
+          } else {
+            console.log(`${c.dim}    Git status: clean${c.reset}`);
+          }
+        }
+      } catch (err) {
+        // Silently ignore git status errors
+      }
+    }
+
     await indexFiles(col.pwd, col.glob_pattern);
     console.log("");
   }
diff --git a/store.test.ts b/src/store.test.ts
similarity index 100%
rename from store.test.ts
rename to src/store.test.ts
diff --git a/store.ts b/src/store.ts
similarity index 100%
rename from store.ts
rename to src/store.ts