diff --git a/client/apollo/css/flat.css b/client/apollo/css/flat.css
index 646a1073a4..04c574a976 100644
--- a/client/apollo/css/flat.css
+++ b/client/apollo/css/flat.css
@@ -1,27 +1,27 @@
-.jbrowse .Flat div.gridline_minor {
+.Flat div.gridline_minor {
 	border: none
 }
-.jbrowse .Flat div.gridline_major {
+.Flat div.gridline_major {
 	border: none
 }
 
-.jbrowse .Flat div.overview {
+.Flat div.overview {
 	background: #f9f9f9;
 }
-.jbrowse .Flat.Dark div.overview {
+.Flat.Dark div.overview {
 	background: #333333;
 	box-shadow: 0 2px 10px 0px #2b2b2b;
 	border: 1px solid black;
 }
 
-.jbrowse .Flat.Dark div.overview-pos{
+.Flat.Dark div.overview-pos{
 	color: white;
 }
 
-.jbrowse .Flat div#static_track{
+.Flat div#static_track{
 	background: #f9f9f9;
 }
-.jbrowse .Flat.Dark div#static_track{
+.Flat.Dark div#static_track{
 	color: white;
 	background: #333333;
 	box-shadow: 0 2px 10px 0px black;
diff --git a/client/apollo/css/genome.css b/client/apollo/css/genome.css
index 42b7acc477..1d7c2ffb66 100644
--- a/client/apollo/css/genome.css
+++ b/client/apollo/css/genome.css
@@ -26,19 +26,19 @@ div.locationThumb {
 
 
 /* tweak the style of the powered_by link that has the WA logo in it */
-.jbrowse .menuBar .powered_by {
+.menuBar .powered_by {
     height: 27px;
     background: white;
     border-right: 1px solid rgb(156,156,156);
     position: relative;
     top: -1px;
 }
-.jbrowse .menuBar .powered_by > img {
+.menuBar .powered_by > img {
     position: relative;
     top: 1px;
 }
 
-.jbrowse .menuBar .user .icon {
+.menuBar .user .icon {
     height: 16px;
     width: 16px;
     margin-right: 2px;
@@ -48,7 +48,7 @@ div.locationThumb {
     background: url("img/glyphs_white.png") no-repeat -168px -27px;
 }
 
-.jbrowse .usericon {
+.usericon {
     height: 16px;
     width: 16px;
     margin-right: 2px;
diff --git a/client/apollo/css/get_history.css b/client/apollo/css/get_history.css
index 7edfe6017d..e2cc1a053c 100644
--- a/client/apollo/css/get_history.css
+++ b/client/apollo/css/get_history.css
@@ -1,68 +1,68 @@
 @CHARSET "UTF-8";
 
-.jbrowse .history_div {
+.history_div {
 	font-size: 9px;
 }
 
-.jbrowse .history_table {
+.history_table {
 	font-size: 1.5em;
 /*	max-width: 47em; */
 }
 
-.jbrowse .history_header_column {
+.history_header_column {
 	font-weight: bold;
 	text-decoration: underline;
 }
-.jbrowse .history_set{
+.history_set{
 	text-align: left;
 	margin-right: auto;
 }
 
-.jbrowse .history_column_operation {
+.history_column_operation {
 	width: 17em !important;
 }
 
-.jbrowse .history_column_action{
+.history_column_action{
 	width: 5em !important;
 }
 
-.jbrowse .history_column {
+.history_column {
 	width: 15em;
 	display: inline-block;
 	background-color: inherit;
 }
 
-.jbrowse .history_row_selected  {
+.history_row_selected  {
 	background-color: #4169e1;
 	color: white;
 }
 
-.jbrowse .history_row:hover  {
+.history_row:hover  {
 	background-color: #000099;
 	color: white;
 }
 
-.jbrowse .history_row_current {
+.history_row_current {
 	background-color: #787878;
 	color: white;
 }
 
-.jbrowse .history_rows {
+.history_rows {
 	max-height: 10em;
 	overflow-y: auto;
 }
 
-.jbrowse .history_column_date {
+.history_column_date {
 	max-width: 10em;
 }
 
-.jbrowse .history_preview {
+.history_preview {
 	width: 45em;
 	height: 2em;
 	padding-top: 3em;
 }
 
-.jbrowse .revert_button.dijitButton .dijitButtonNode {
+.revert_button.dijitButton .dijitButtonNode {
 	padding: 0px;
 	margin: 0px;
 }
diff --git a/client/apollo/css/get_sequence.css b/client/apollo/css/get_sequence.css
index d6efb6201d..f4597ce030 100644
--- a/client/apollo/css/get_sequence.css
+++ b/client/apollo/css/get_sequence.css
@@ -1,35 +1,35 @@
 @CHARSET "UTF-8";
 
-.jbrowse .get_sequence {
+.get_sequence {
 	font-size:10px;
 }
 
-.jbrowse .gff3_area{
+.gff3_area{
 	width: 50em;
 	height: 20em;
 	font-family: 'courier';
 	font-size: 1.0em;
 }
 
-.jbrowse .sequence_area {
+.sequence_area {
 	width: 60em;
 	height: 20em;
 	font-family: 'courier';
 	font-size: 1.5em;
 }
 
-.jbrowse .first_button_div {
+.first_button_div {
 	margin-top: 10px;
 }
 
-.jbrowse .button_div {
+.button_div {
 	margin-top: 5px;
 }
 
-.jbrowse .button_label {
+.button_label {
 	margin-left: 3px;
 }
 
-.jbrowse .button_field {
+.button_field {
 	margin-left: 3px;
 }
\ No newline at end of file
diff --git a/client/apollo/css/maker_darkbackground.css b/client/apollo/css/maker_darkbackground.css
index 2c3ceb4db5..47c9dab687 100644
--- a/client/apollo/css/maker_darkbackground.css
+++ b/client/apollo/css/maker_darkbackground.css
@@ -1,166 +1,166 @@
 /* styles for MAKER tracks and additional customization of WebApollo */
-.jbrowse .Dark .track_jbrowse_view_track_wiggle_xyplot .canvas-track {
+.Dark .track_jbrowse_view_track_wiggle_xyplot .canvas-track {
     background-color: hsla(240, 2%, 18%, 1);
 }
 
-.jbrowse .Dark .track_jbrowse_view_track_wiggle_density .canvas-track {
+.Dark .track_jbrowse_view_track_wiggle_density .canvas-track {
     background-color: hsla(240, 2%, 18%, 1);
 }
-.jbrowse .Dark .wigglePositionIndicator {
+.Dark .wigglePositionIndicator {
 	background: white;
 }
 
-.jbrowse .Dark div.track  {
+.Dark div.track  {
     /* based on CoolWorld color palette from kuler.adobe.com */
     /*background-color: #142933;*/
     border:0px;
 }
-.jbrowse .Dark .sequence_blur {
+.Dark .sequence_blur {
     background-color: #999;
 }
-.jbrowse .Dark div.pin_underlay {
+.Dark div.pin_underlay {
     background-color: #142933;
 }
 
 
-.jbrowse .Dark div.outerTrackContainer {
+.Dark div.outerTrackContainer {
     background-color: rgb(59, 59, 61);
 }
 
 
-.jbrowse .Dark div.gridline_major {
+.Dark div.gridline_major {
     border-color : rgb(41,40,38);
 }
 
-.jbrowse .Dark div.gridline_minor {
+.Dark div.gridline_minor {
     border-color : rgba(96,96, 104, 0.72);
 }
 
 
-.jbrowse .Dark div#overviewtrack_overview_loc_track {
+.Dark div#overviewtrack_overview_loc_track {
     background-color: transparent;
 }
 
-.jbrowse .Dark div#gridtrack {
+.Dark div#gridtrack {
     background-color: transparent;
 }
 
 
-.jbrowse .Dark .feature-name {
+.Dark .feature-name {
     color: #FAFFF9;
 }
 
-.jbrowse .Dark div.feature-description {
+.Dark div.feature-description {
     color: #bbb;
 }
 /* UI elements */
-.jbrowse .Dark div.locationTrap {
+.Dark div.locationTrap {
     background-color: #929292;
 	border-bottom-color: #0b2648;
 }
 
-.jbrowse .Dark .pin_underlay.track.block {
+.Dark .pin_underlay.track.block {
     background-color: rgb(59, 59, 61);
 }
 
-.jbrowse .Dark .dna-residues.forward-strand,
-.jbrowse .Dark .dna-residues.reverse-strand {
+.Dark .dna-residues.forward-strand,
+.Dark .dna-residues.reverse-strand {
     background-color: transparent;
 }
 
-.jbrowse .Dark div.wa-sequence .dna-residues.forward-strand {
+.Dark div.wa-sequence .dna-residues.forward-strand {
     color: rgb(240, 240, 240);
     z-index: 5;
 }
 
-.jbrowse .Dark div.wa-sequence .dna-residues.reverse-strand {
+.Dark div.wa-sequence .dna-residues.reverse-strand {
     color: rgb(170, 169, 169);
     z-index: 5;
 }
 /*  nucleotide alignments from MAKER */
-.jbrowse .Dark .blastn-part,
-.jbrowse .Dark .plus-blastn-part,
-.jbrowse .Dark .minus-blastn-part  {
+.Dark .blastn-part,
+.Dark .plus-blastn-part,
+.Dark .minus-blastn-part  {
     background-color: rgb(102,204,0);
 }
 
-.jbrowse .Dark .est2genome-part,
-.jbrowse .Dark .plus-est2genome-part,
-.jbrowse .Dark .minus-est2genome-part   {
+.Dark .est2genome-part,
+.Dark .plus-est2genome-part,
+.Dark .minus-est2genome-part   {
     background-color: rgb(250,250,210);
 }
 
-.jbrowse .Dark .est_gff-part,
-.jbrowse .Dark .plus-est_gff-part,
-.jbrowse .Dark .minus-est_gff-part  {
+.Dark .est_gff-part,
+.Dark .plus-est_gff-part,
+.Dark .minus-est_gff-part  {
     background-color: rgb(251,255,179);
 }
 
-.jbrowse .Dark .mike-repeat-part,
-.jbrowse .Dark .plus-mike-repeat-part,
-.jbrowse .Dark .minus-mike-repeat-part  {
+.Dark .mike-repeat-part,
+.Dark .plus-mike-repeat-part,
+.Dark .minus-mike-repeat-part  {
     background-color: rgb(255,0,0);
 }
 
-.jbrowse .Dark .mike-snap-part,
-.jbrowse .Dark .plus-mike-snap-part,
-.jbrowse .Dark .minus-mike-snap-part  {
+.Dark .mike-snap-part,
+.Dark .plus-mike-snap-part,
+.Dark .minus-mike-snap-part  {
     background-color: rgb(153,255,204);
 }
 
-.jbrowse .Dark .mike-augustus-part,
-.jbrowse .Dark .plus-mike-augustus-part,
-.jbrowse .Dark .minus-mike-augustus-part  {
+.Dark .mike-augustus-part,
+.Dark .plus-mike-augustus-part,
+.Dark .minus-mike-augustus-part  {
     background-color: rgb(255,204,255);
 }
 
 /*  protein alignments from MAKER */
-.jbrowse .Dark .blastx-part,
-.jbrowse .Dark .plus-blastx-part,
-.jbrowse .Dark .minus-blastx-part  {
+.Dark .blastx-part,
+.Dark .plus-blastx-part,
+.Dark .minus-blastx-part  {
     background-color: pink;
 }
 
-.jbrowse .Dark .protein2genome-part,
-.jbrowse .Dark .plus-protein2genome-part,
-.jbrowse .Dark .minus-protein2genome-part  {
+.Dark .protein2genome-part,
+.Dark .plus-protein2genome-part,
+.Dark .minus-protein2genome-part  {
     background-color: rgb(255,255,0);
 }
 
 /* ???? not found in gff3.tiers
-.jbrowse .Dark .protein_gff-part,
-.jbrowse .Dark .plus-protein_gff-part,
-.jbrowse .Dark .minus-protein_gff-part  {
+.Dark .protein_gff-part,
+.Dark .plus-protein_gff-part,
+.Dark .minus-protein_gff-part  {
 }
 */
 
-.jbrowse .Dark .tblastx-part,
-.jbrowse .Dark .plus-tblastx-part,
-.jbrowse .Dark .minus-tblastx-part  {
+.Dark .tblastx-part,
+.Dark .plus-tblastx-part,
+.Dark .minus-tblastx-part  {
     background-color: rgb(102,51,102);
 }
 
 /*  ????  couldn't find in gff3.tiers
-.jbrowse .Dark .cdna2genome-part,
-.jbrowse .Dark .plus-cdna2genome-part,
-.jbrowse .Dark .minus-cdna2genome-part  {
+.Dark .cdna2genome-part,
+.Dark .plus-cdna2genome-part,
+.Dark .minus-cdna2genome-part  {
 }
 */
 
 /*  ????  couldn't find in gff3.tiers
-.jbrowse .Dark .altest_gff-part,
-.jbrowse .Dark .plus-altest_gff-part,
-.jbrowse .Dark .minus-altest_gff-part  {
+.Dark .altest_gff-part,
+.Dark .plus-altest_gff-part,
+.Dark .minus-altest_gff-part  {
 }
 */
 
-.jbrowse .Dark .maker-CDS  {
+.Dark .maker-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(51,102,255);
 }
 
-.jbrowse .Dark .maker-UTR {
+.Dark .maker-UTR {
     height: 80%;
     top: 10%;
     border-style: solid;
@@ -169,13 +169,13 @@
     background-color: #142933;
 }
 
-.jbrowse .Dark .upd-CDS  {
+.Dark .upd-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(0,204,0);
 }
 
-.jbrowse .Dark .upd-UTR {
+.Dark .upd-UTR {
     height: 80%;
     top: 10%;
     border-style: solid;
@@ -184,13 +184,13 @@
     background-color: #142933;
 }
 
-.jbrowse .Dark .TAIR-CDS  {
+.Dark .TAIR-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(255,140,0);
 }
 
-.jbrowse .Dark .TAIR-UTR {
+.Dark .TAIR-UTR {
     height: 80%;
     top: 10%;
     border-style: solid;
@@ -199,13 +199,13 @@
     background-color: #142933;
 }
 
-.jbrowse .Dark .TAIR-CDS  {
+.Dark .TAIR-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(255,140,0);
 }
 
-.jbrowse .Dark .TAIR-UTR {
+.Dark .TAIR-UTR {
     height: 80%;
     top: 10%;
     border-style: solid;
@@ -214,37 +214,37 @@
     background-color: #142933;
 }
 
-.jbrowse .Dark .psu-CDS  {
+.Dark .psu-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(153,0,76);
 }
 
-.jbrowse .Dark .psu-UTR {
+.Dark .psu-UTR {
     height: 80%;
     top: 10%;
     background-color: rgb(153,0,76);
 }
 
-.jbrowse .Dark .nc-CDS  {
+.Dark .nc-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(255,0,127);
 }
 
-.jbrowse .Dark .nc-UTR {
+.Dark .nc-UTR {
     height: 80%;
     top: 10%;
     background-color: rgb(255,0,127);
 }
 
-.jbrowse .Dark .alt-CDS  {
+.Dark .alt-CDS  {
     height: 80%;
     top: 10%;
     background-color: rgb(138,43,226);
 }
 
-.jbrowse .Dark .alt-UTR {
+.Dark .alt-UTR {
     height: 80%;
     top: 10%;
     border-style: solid;
@@ -254,26 +254,26 @@
 }
 
 
-.jbrowse .Dark .snap-CDS {
+.Dark .snap-CDS {
     height: 80%;
     top: 10%;
     background-color: rgb(153,255,204);
 }
 
-.jbrowse .Dark .snap-UTR {
+.Dark .snap-UTR {
     height: 80%;
     top: 10%;
     border: 1px solid rgb(153,255,204);
     background-color: #142933;
 }
 
-.jbrowse .Dark .genemark-CDS {
+.Dark .genemark-CDS {
     height: 80%;
     top: 10%;
     background-color: rgb(103,155,104);
 }
 
-.jbrowse .Dark .genemark-UTR {
+.Dark .genemark-UTR {
     height: 80%;
     top: 10%;
     border: 1px solid rgb(103,155,104);
@@ -281,12 +281,12 @@
 }
 
 /* ???? not sure about pred_gff, same as GeneMark?
-.jbrowse .Dark .pred_gff-CDS {
+.Dark .pred_gff-CDS {
     height: 80%;
     top: 10%;
     background-color: rgb(103,155,104);
 }
-.jbrowse .Dark .pred_gff-UTR {
+.Dark .pred_gff-UTR {
     height: 80%;
     top: 10%;
     border: 1px solid rgb(103,155,104);
@@ -295,9 +295,9 @@
 */
 
 /* ???? couldn't find model_gff in gff3.tiers
-.jbrowse .Dark .model_gff-CDS {
+.Dark .model_gff-CDS {
 }
-.jbrowse .Dark .model_gff-UTR {
+.Dark .model_gff-UTR {
     height: 80%;
     top: 10%;
     border: 1px solid rgb(103,155,104);
@@ -305,13 +305,13 @@
 }
 */
 
-.jbrowse .Dark .fgenesh-CDS {
+.Dark .fgenesh-CDS {
     height: 80%;
     top: 10%;
     background-color: rgb(55,153,255);
 }
 
-.jbrowse .Dark .fgenesh-UTR {
+.Dark .fgenesh-UTR {
     height: 80%;
     top: 10%;
     /*    background-color: rgb(255,204,255); */
@@ -326,30 +326,30 @@
 
 /*  ???? repeatrunner is different than repeatmasker in gff3.tiers,
     should we make it different also for webapollo?
-.jbrowse .Dark .repeatrunner,
-.jbrowse .Dark .plus-repeatrunner,
-.jbrowse .Dark .minus-repeatrunner  {
+.Dark .repeatrunner,
+.Dark .plus-repeatrunner,
+.Dark .minus-repeatrunner  {
 }
 */
 
-.jbrowse .Dark .left-edge-match  {
+.Dark .left-edge-match  {
     border-left: solid black 2px !important;
 }
 
-.jbrowse .Dark .right-edge-match  {
+.Dark .right-edge-match  {
     border-right: solid black 2px !important;
 }
 
-.jbrowse .Dark .selected-annotation {
+.Dark .selected-annotation {
 	outline-color: black;
 }
 
 /* start NeatHTMLFeatures styles */
 
-.jbrowse .Dark div.neat-UTR {
+.Dark div.neat-UTR {
     background-color: #DDD;
 }
-.jbrowse .Dark polyline.neat-intron {
+.Dark polyline.neat-intron {
     stroke: lightgrey;
 }
 /* end NeatHTMLFeatures styles */
diff --git a/client/apollo/css/search_sequence.css b/client/apollo/css/search_sequence.css
index 59167f48a4..91260bbbae 100644
--- a/client/apollo/css/search_sequence.css
+++ b/client/apollo/css/search_sequence.css
@@ -1,37 +1,37 @@
 @CHARSET "UTF-8";
 
-.jbrowse .search_sequence_label {
+.search_sequence_label {
 	font-size: 1.5em;
 }
 
-.jbrowse .search_sequence_input {
+.search_sequence_input {
 	width: 50em;
 	height: 3.5em;
 }
 
-.jbrowse .search_sequence_area {
+.search_sequence_area {
 	margin-bottom: 10px;
 }
 
-.jbrowse .search_all_ref_seqs_area {
+.search_all_ref_seqs_area {
 	margin-top: 5px;
 	margin-bottom: 5px;
 }
 
-.jbrowse .search_all_ref_seqs_checkbox {
+.search_all_ref_seqs_checkbox {
 	margin-right: 3px;
 }
 
-.jbrowse .search_all_ref_seqs_label {
+.search_all_ref_seqs_label {
 	font-size: 1em;
 }
 
-.jbrowse .search_sequence_matches_row:hover {
+.search_sequence_matches_row:hover {
 	background-color: #000099;
 	color: white;
 }
 
-.jbrowse .search_sequence_matches_generic_field {
+.search_sequence_matches_generic_field {
 	width: 6.3em;
 	margin-right: 0.2em;
 	overflow: hidden;
@@ -41,11 +41,11 @@
 	display: table-cell;
 }
 
-.jbrowse .search_sequence_matches_header {
+.search_sequence_matches_header {
 	margin-bottom: 10px;
 }
 
-.jbrowse .search_sequence_matches_field {
+.search_sequence_matches_field {
 	margin-top: 0px;
 	margin-bottom: 0px;
 	float: left;
@@ -53,24 +53,24 @@
 	width: 6em;
 }
 
-.jbrowse .search_sequence_tools {
+.search_sequence_tools {
 	margin-bottom: 10px;
 }
 
-.jbrowse .search_sequence_matches {
+.search_sequence_matches {
 	max-height: 25em;
 	overflow: auto;
 }
 
-.jbrowse .search_sequence_matches_row {
+.search_sequence_matches_row {
 	display: table-row;
 }
 
 
-.jbrowse .search_sequence_message {
+.search_sequence_message {
 	font-size: 1.6em;
 }
 
-.jbrowse .search_sequence {
+.search_sequence {
 	font-size: 9px;
 }
diff --git a/docs/Apollo2Build.md b/docs/Apollo2Build.md
index 3adac246f8..a0f33f0b3d 100644
--- a/docs/Apollo2Build.md
+++ b/docs/Apollo2Build.md
@@ -81,9 +81,10 @@ Updating the web-service doc can be done with `./apollo create-rest-doc`
 
 #### Running the code for the making client plugin changes
 
-After starting the server run `./apollo watchman` which should automatically copy any files that have been modified from the [client directory](../client) to the running instance.
+After starting the server you can run `./gradlew installJBrowseWebOnly` to update the client code to update the JS code. 
+
+If for some reason this is not working then make sure that your network development tab, in your browser console, has disabled caching.  You can also run the command `./gradlew copy-resources-dev` manually each time instead if the files don't seem to be getting copied.
 
-If for some reason this is not working then make sure that your network development tab, in your browser console, has disabled caching.  You can also run the command `gradle copy-resources-dev` manually each time instead if the files don't seem to be getting copied.
 
 #### Running the code for GWT changes