diff --git a/js/CTSnapshot.js b/js/CTSnapshot.js
index 96761d2..cfd3d8e 100644
--- a/js/CTSnapshot.js
+++ b/js/CTSnapshot.js
@@ -14,13 +14,9 @@ const deleteDirectory = require( '../../perennial/js/common/deleteDirectory' );
 const execute = require( '../../perennial/js/common/execute' );
 const getRepoList = require( '../../perennial/js/common/getRepoList' );
 const gitRevParse = require( '../../perennial/js/common/gitRevParse' );
-const npmCommand = require( '../../perennial/js/common/npmCommand' );
 const fs = require( 'fs' );
 const _ = require( 'lodash' ); // eslint-disable-line
 
-// constants
-const copyOptions = { filter: path => path.indexOf( 'node_modules' ) < 0 };
-
 class CTSnapshot {
   /**
    * Creates this snapshot.
@@ -76,8 +72,8 @@ class CTSnapshot {
     }
 
     for ( const repo of this.repos ) {
-      await copyDirectory(  `${rootDir}/${repo}`, `${this.phetDir}/${repo}`, copyOptions );
-      await copyDirectory(  `${rootDir}/${repo}`, `${this.phetioDir}/${repo}`, copyOptions );
+      await copyDirectory(  `${rootDir}/${repo}`, `${this.phetDir}/${repo}`, {} );
+      await copyDirectory(  `${rootDir}/${repo}`, `${this.phetioDir}/${repo}`, {} );
     }
 
     // @public {Array.<Object>}
@@ -100,16 +96,6 @@ class CTSnapshot {
     } );
   }
 
-  async npmInstall() {
-    const npmRepos = this.repos.filter( repo => fs.existsSync( `../${repo}/package.json` ) );
-    for ( const repo of npmRepos ) {
-      this.setSnapshotStatus( `Running npm update for ${repo}` );
-
-      await execute( npmCommand, [ 'update', `--cache=../npm-caches/${repo}`, '--tmp=../npm-tmp' ], `${this.phetDir}/${repo}` );
-      await execute( npmCommand, [ 'update', `--cache=../npm-caches/${repo}`, '--tmp=../npm-tmp' ], `${this.phetioDir}/${repo}` );
-    }
-  }
-
   /**
    * Removes the snapshot's files.
    * @public
diff --git a/js/local-server.js b/js/local-server.js
index e819213..b79d32e 100644
--- a/js/local-server.js
+++ b/js/local-server.js
@@ -11,7 +11,9 @@ const cloneMissingRepos = require( '../../perennial/js/common/cloneMissingRepos'
 const getRepoList = require( '../../perennial/js/common/getRepoList' );
 const gitPull = require( '../../perennial/js/common/gitPull' );
 const isStale = require( '../../perennial/js/common/isStale' );
+const npmUpdate = require( '../../perennial/js/common/npmUpdate' );
 const CTSnapshot = require( './CTSnapshot' );
+const fs = require( 'fs' );
 const http = require( 'http' );
 const _ = require( 'lodash' ); // eslint-disable-line
 const path = require( 'path' );
@@ -297,7 +299,14 @@ const cycleSnapshots = async () => {
         for ( const repo of staleRepos ) {
           await gitPull( repo );
         }
-        await cloneMissingRepos();
+        const clonedRepos = await cloneMissingRepos();
+
+        // npm prune/update on any changed repos, so we can keep our npm status good in our checked out version
+        for ( const repo of [ ...staleRepos, ...clonedRepos ] ) {
+          if ( fs.existsSync( `../${repo}/package.json` ) ) {
+            await npmUpdate( repo );
+          }
+        }
       }
       else {
         winston.info( 'No stale repos' );
@@ -312,8 +321,6 @@ const cycleSnapshots = async () => {
 
           snapshots.unshift( snapshot );
 
-          await snapshot.npmInstall();
-
           const cutoffTimestamp = Date.now() - 1000 * 60 * 60 * 24 * NUMBER_OF_DAYS_TO_KEEP_SNAPSHOTS;
           while ( snapshots.length > 70 || snapshots[ snapshots.length - 1 ].timestamp < cutoffTimestamp && !snapshots[ snapshots.length - 1 ].exists ) {
             removeResultsForSnapshot( testResults, snapshots.pop() );