Don't do dangerous operations without --force

src/cli.ts

@@ -121,8 +121,17 @@ const optionDefinitions: commandLineArgs.OptionDefinition[] = [
   {
     name: 'clear',
     type: Boolean,
+    defaultValue: false,
     description: 'Clear the out directory (if one exists) before running.',
   },
+  {
+    name: 'force',
+    type: Boolean,
+    defaultValue: false,
+    description:
+        `If given, may overwrite or delete files when converting the given ` +
+        `input directory.`,
+  },
 ];
 
 interface Options {
@@ -140,6 +149,7 @@ interface Options {
   'workspace-dir'?: string;
   'github-token'?: string;
   'prerelease-version'?: string;
+  force: boolean;
 }
 
 export async function run() {
@@ -196,6 +206,17 @@ installation.
     return;
   }
 
+  // Ok, we're updating a package in a directory not under our control.
+  // We need to be sure it's safe. In a future PR let's check with git, but
+  // for now, we'll ask the user to pass in a --force flag.
+  if (!options.force) {
+    console.error(
+        `When running modulizer on an existing directory, ` +
+        `be sure that all changes are checked into source control. ` +
+        `Run with --force once you've verified.`);
+    process.exit(1);
+  }
+
   // TODO: each file is not always needed, refactor to optimize loading
   let inBowerJson: {name: string, version: string, main: any}|undefined;
   let inPackageJson: {name: string, version: string}|undefined;