diff --git a/.gitignore b/.gitignore
index 55dd4d05c14..91f6c027723 100644
--- a/.gitignore
+++ b/.gitignore
@@ -153,7 +153,7 @@ static/plugins
 static/scripts
 node_modules
 bower_components
-client/galaxy/scripts/libs/*
+client/src/libs/*
 client/galaxy/style/less/*
 
 # Documentation build files.
diff --git a/client/.eslintignore b/client/.eslintignore
index 5dc007acedc..b913d99c342 100644
--- a/client/.eslintignore
+++ b/client/.eslintignore
@@ -1,6 +1,6 @@
 *.test.js
-galaxy/scripts/qunit
-galaxy/scripts/mocha
-galaxy/scripts/libs
-galaxy/scripts/nls
-galaxy/scripts/legacy
+src/qunit
+src/mocha
+src/libs
+src/nls
+src/legacy
diff --git a/client/README.md b/client/README.md
index 46ae25f4a65..4a81854af4d 100644
--- a/client/README.md
+++ b/client/README.md
@@ -175,7 +175,7 @@ following commands.
 ## Writing a test file
 
 The karma configs are setup to look at any file ending in "*.test.js". Please
-place your test files inside client/galaxy/scripts folders right next to
+place your test files inside client/src folders right next to
 whatever files that they are testing.
 
 ```javascript
@@ -301,13 +301,13 @@ broken up into easily testable chunks.
 
 ## Specific test scenarios & examples
 
-[Mocking an imported dependency](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/tagService.test.js)
+[Mocking an imported dependency](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/tagService.test.js)
 
-[Testing async operations](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/tagService.test.js)
+[Testing async operations](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/tagService.test.js)
 
-[Testing a Vue component for expected rendering output](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/StatelessTags.test.js)
+[Testing a Vue component for expected rendering output](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/StatelessTags.test.js)
 
-[Firing an event against a shallow mounted vue component](https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/components/Tags/StatelessTags.test.js)
+[Firing an event against a shallow mounted vue component](https://github.com/galaxyproject/galaxy/blob/dev/client/src/components/Tags/StatelessTags.test.js)
 
 
 ## The dirty secret about testing
diff --git a/client/gulpfile.js b/client/gulpfile.js
index 2796429de4b..fe752b522d8 100644
--- a/client/gulpfile.js
+++ b/client/gulpfile.js
@@ -35,13 +35,13 @@ const paths = {
         requirejs: ["require.js", "require.js"],
         underscore: ["underscore.js", "underscore.js"],
     },
-    libs: ["galaxy/scripts/libs/**/*.js"],
+    libs: ["src/libs/**/*.js"],
 };
 
 function stageLibs(callback) {
     Object.keys(paths.lib_locs).forEach((lib) => {
         var p1 = path.resolve(path.join(paths.node_modules, lib, paths.lib_locs[lib][0]));
-        var p2 = path.resolve(path.join("galaxy", "scripts", "libs", paths.lib_locs[lib][1]));
+        var p2 = path.resolve(path.join("src", "libs", paths.lib_locs[lib][1]));
         if (fs.existsSync(p1)) {
             del.sync(p2);
             fs.createReadStream(p1).pipe(fs.createWriteStream(p2));
diff --git a/client/karma/karma.config.base.js b/client/karma/karma.config.base.js
index 0b77a81245b..368a6551446 100644
--- a/client/karma/karma.config.base.js
+++ b/client/karma/karma.config.base.js
@@ -12,7 +12,7 @@ module.exports = config => {
     });
 
     return {
-        basePath: "../galaxy/scripts",
+        basePath: "../src",
         browsers: ["ChromeHeadlessNoSandbox"],
         client: {
             captureConsole: true
diff --git a/client/package.json b/client/package.json
index 844c8b33cbe..0da185fd18b 100644
--- a/client/package.json
+++ b/client/package.json
@@ -75,15 +75,15 @@
     "webpack-production-maps": "GXY_BUILD_SOURCEMAPS=1 webpack -p",
     "gulp": "gulp",
     "save-build-hash": "(git rev-parse HEAD 2>/dev/null || echo '') >../static/client_build_hash.txt",
-    "prettier": "prettier --write 'galaxy/style/scss/**/*.scss' 'galaxy/scripts/**/{*.js,*.vue}' '!galaxy/scripts/libs/**'",
-    "prettier-check": "prettier --check 'galaxy/style/scss/**/*.scss' 'galaxy/scripts/**/{*.js,*.vue}' '!galaxy/scripts/libs/**'",
+    "prettier": "prettier --write 'galaxy/style/scss/**/*.scss' 'src/**/{*.js,*.vue}' '!src/libs/**'",
+    "prettier-check": "prettier --check 'galaxy/style/scss/**/*.scss' 'src/**/{*.js,*.vue}' '!src/libs/**'",
     "styleguide": "vue-styleguidist server",
     "styleguide:build": "vue-styleguidist build",
     "test": "yarn run test-mocha && yarn run test-qunit",
     "test-watch": "yarn run test-mocha --no-single-run",
     "test-qunit": "karma start karma/karma.config.qunit.js",
     "test-mocha": "karma start karma/karma.config.mocha.js",
-    "eslint": "eslint -c .eslintrc.js galaxy/scripts --ext .js,.vue"
+    "eslint": "eslint -c .eslintrc.js src --ext .js,.vue"
   },
   "devDependencies": {
     "@babel/core": "^7.10.1",
diff --git a/client/src/components/RuleCollectionBuilder.vue b/client/src/components/RuleCollectionBuilder.vue
index fc90ace0352..59dc8e56cb7 100644
--- a/client/src/components/RuleCollectionBuilder.vue
+++ b/client/src/components/RuleCollectionBuilder.vue
@@ -1690,7 +1690,7 @@ export default {
 };
 </script>
 
-<style src="../../../node_modules/handsontable/dist/handsontable.full.css"></style>
+<style src="../../node_modules/handsontable/dist/handsontable.full.css"></style>
 <style>
 .table-column {
     width: 100%;
diff --git a/client/src/utils/localization.js b/client/src/utils/localization.js
index 13aec2df0b8..b8f81892334 100644
--- a/client/src/utils/localization.js
+++ b/client/src/utils/localization.js
@@ -1,7 +1,7 @@
 // eslint-disable-next-line no-undef
 define(["i18n!nls/locale"], function (localeStrings) {
     // =============================================================================
-    /** Simple string replacement localization. Language data from galaxy/scripts/nls */
+    /** Simple string replacement localization. Language data from src/nls */
 
     if (Object.prototype.hasOwnProperty.call(localeStrings, "__root")) {
         //console.debug( 'amdi18n+webpack localization for ' + locale + ' loaded' );
diff --git a/client/styleguide.config.js b/client/styleguide.config.js
index 60394c96699..f2174ed27cd 100644
--- a/client/styleguide.config.js
+++ b/client/styleguide.config.js
@@ -34,7 +34,7 @@ const sections = [
         name: "Components",
         // Components that are directories will get their own section
         sections: glob
-            .sync("./galaxy/scripts/components/*")
+            .sync("./src/components/*")
             .map((file) => {
                 if (fs.lstatSync(file).isDirectory()) {
                     return {
@@ -45,7 +45,7 @@ const sections = [
             })
             .filter((v) => v),
         // ...while top level components are handled here.
-        components: "./galaxy/scripts/components/*.vue",
+        components: "./src/components/*.vue",
     },
 ];
 
@@ -53,6 +53,6 @@ module.exports = {
     webpackConfig,
     pagePerSection: true,
     sections,
-    require: ["./galaxy/style/scss/base.scss", "./galaxy/scripts/polyfills.js", "./galaxy/scripts/bundleEntries.js"],
-    vuex: "./galaxy/scripts/store/index.js",
+    require: ["./galaxy/style/scss/base.scss", "./src/polyfills.js", "./src/bundleEntries.js"],
+    vuex: "./src/store/index.js",
 };
diff --git a/client/webpack.config.js b/client/webpack.config.js
index 579574c8420..237c793cce3 100644
--- a/client/webpack.config.js
+++ b/client/webpack.config.js
@@ -6,7 +6,7 @@ const OptimizeCssAssetsPlugin = require("optimize-css-assets-webpack-plugin");
 const MiniCssExtractPlugin = require("mini-css-extract-plugin");
 const DuplicatePackageCheckerPlugin = require("duplicate-package-checker-webpack-plugin");
 
-const scriptsBase = path.join(__dirname, "galaxy/scripts");
+const scriptsBase = path.join(__dirname, "src");
 const libsBase = path.join(scriptsBase, "libs");
 const styleBase = path.join(__dirname, "galaxy/style");
 const imageBase = path.join(__dirname, "../static/style");
diff --git a/config/plugins/visualizations/scatterplot/src/scatterplot.js b/config/plugins/visualizations/scatterplot/src/scatterplot.js
index 0cc89e940d3..8124b8e6b58 100644
--- a/config/plugins/visualizations/scatterplot/src/scatterplot.js
+++ b/config/plugins/visualizations/scatterplot/src/scatterplot.js
@@ -4,8 +4,8 @@ import "./jqglobals";
 import * as Backbone from "backbone";
 import * as d3 from "d3";
 import * as _ from "underscore";
-import "../../../../../client/galaxy/scripts/ui/peek-column-selector";
-import "../../../../../client/galaxy/scripts/ui/pagination";
+import "../../../../../client/src/ui/peek-column-selector";
+import "../../../../../client/src/ui/pagination";
 import "jquery-ui-bundle";
 import "bootstrap";
 
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index c30c71da4e5..499c9ea7d72 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1563,7 +1563,7 @@
 
 :Description:
     Default localization for Galaxy UI. Allowed values are listed at
-    the end of client/galaxy/scripts/nls/locale.js. With the default
+    the end of client/src/nls/locale.js. With the default
     value (auto), the locale will be automatically adjusted to the
     user's navigator language. Users can override this settings in
     their user preferences if the localization settings are enabled in
diff --git a/doc/source/api_doc.rst b/doc/source/api_doc.rst
index 622772832fb..379cb8d006b 100644
--- a/doc/source/api_doc.rst
+++ b/doc/source/api_doc.rst
@@ -18,7 +18,7 @@ The Galaxy API addresses these and other situations by exposing Galaxy
 internals through an additional interface, known as an Application Programming
 Interface, or API.
 
-Various language specific bindings for interfacing with the Galaxy API have been developed by the Galaxy community including `Python <https://bioblend.readthedocs.io/>`__, `PHP <https://github.com/galaxyproject/blend4php>`__, `Java <https://github.com/jmchilton/blend4j>`__, and `JavaScript <https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc>`__.
+Various language specific bindings for interfacing with the Galaxy API have been developed by the Galaxy community including `Python <https://bioblend.readthedocs.io/>`__, `PHP <https://github.com/galaxyproject/blend4php>`__, `Java <https://github.com/jmchilton/blend4j>`__, and `JavaScript <https://github.com/galaxyproject/galaxy/tree/dev/client/src/mvc>`__.
 
 Overview of available API resources is available at https://galaxyproject.org/develop/api/ .
 
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index 5eda281b6aa..60ab1d709f7 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -836,7 +836,7 @@ galaxy:
   #user_preferences_extra_conf_path: user_preferences_extra_conf.yml
 
   # Default localization for Galaxy UI. Allowed values are listed at the
-  # end of client/galaxy/scripts/nls/locale.js. With the default value
+  # end of client/src.js. With the default value
   # (auto), the locale will be automatically adjusted to the user's
   # navigator language. Users can override this settings in their user
   # preferences if the localization settings are enabled in
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 06a03fb0325..994fb4d9658 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -1170,7 +1170,7 @@ mapping:
         required: false
         desc: |
           Default localization for Galaxy UI.
-          Allowed values are listed at the end of client/galaxy/scripts/nls/locale.js.
+          Allowed values are listed at the end of client/src.js.
           With the default value (auto), the locale will be automatically adjusted to
           the user's navigator language.
           Users can override this settings in their user preferences if the localization
diff --git a/run_tests.sh b/run_tests.sh
index 888b1418067..bfba8017727 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -42,7 +42,7 @@ The main test types are as follows:
 - Unit: These are Python unit tests either defined as doctests or inside of
    test/unit. These should generally not require a Galaxy instance and should
    quickly test just a component or a few components of Galaxy's backend code.
-- QUnit: These are JavaScript unit tests defined in client/galaxy/scripts/qunit.
+- QUnit: These are JavaScript unit tests defined in client/src/qunit.
 - Selenium: These are full stack tests meant to test the Galaxy UI with real
    browsers and are located in lib/galaxy_test/selenium.
 - ToolShed: These are web tests that use the older Python web testing