Greetings,

I recently tried to upgrading my Jenkins instance from 1.542 to 1.609.1 - 
about a 1.5 year difference in release dates. The jenkins instance is setup 
in a linux-tomcat7 environment described 
here: https://wiki.jenkins-ci.org/display/JENKINS/Tomcat

I performed the upgrade by replacing the ROOT.war to the 1.609.1 WAR file, 
removing the expanded WAR, and restarting tomcat7. The restart took a 
while(~ 1 hour) due 
to https://wiki.jenkins-ci.org/display/JENKINS/JENKINS-24380+Migration
Everything seemed to work fine, but the UI was missing some sections:

The entire left column on the home page was missing (New Job, build queue, 
executors). For a Job (maven job in this case), the only thing visible was 
the Permalinks section. Functionally, the job built successfully though. I 
didn't notice any exceptions being thrown when accessing these pages in the 
log. I created a new job and it was missing the same areas as the existing 
ones.

I wanted to see if a fresh jenkins instance of this version worked so I 
moved my jenkins home somewhere else and restarted tomcat. The fresh 
instance worked fine...which leans towards an issue with an existing plugin 
maybe? I'll attach the versions of all the plugins that were installed. I 
ended up downgrading the jenkins version back to 1.542 (doing the reverse 
migration steps) and it's back to normal.

Questions
1) Has anyone encountered an issue like this?
2) When performing an upgrade, is it recommended to do smaller version 
jumps?
3) Any suggestions on how to proceed?

I have a hunch that the issue is purely css...possible from the 
simple-theme-plugin. The plugin uses this css file:
body {
  background-color: #205081;
}

table, form, input, td, th, p, textarea, select {
  font-family: 'Lucida Grande', 'Segoe UI', Arial, sans-serif;
  font-size: 11px;  
}

pre, .settings-input {
  font-family: Consolas, monospace;
}

h1, h2, h3, h4, h5, h6 {
  color: #000000; }

a:link, a:visited {
  text-decoration: underline;
  color: #3b73af;
}

a.model-link.inside {
  text-decoration:none;
}

#executors a.model-link.inside {
  background: none repeat scroll 0 0 #F5F5F5;
  border: 1px solid #CCCCCC;
  color: #3B73AF;
  display: inline-block;
  font-size: 11px;
  font-weight: normal;
  line-height: 1.3;
  margin: 0 3px 0 0;
  max-width: 100%;
  padding: 1px 5px;
  text-align: left;
  text-decoration: none;
  vertical-align: middle;
  white-space: normal;
}
/*
img {
  display: none;
}
*/

/* top panel */

#top-panel {
  background: none; 
}

#top-panel td#login-field span a {
  background: none; 
}

#top-panel td #searchform a {
  background: none;
  height: auto;
  width: auto; 
}

#top-panel td > a {
  background: url("/userContent/theme/jenkins_logo.png") 0 no-repeat;
  display: block;
  width: 330px;
  height: 30px;
  margin: 8px 0 5px 10px; 
}

#top-panel td > a img {
  display: none; 
}

#top-panel img {
  display: none;
}

/* project status */

#projectstatus {
  background: #fff; 
}

#projectstatus tr:nth-of-type(odd) {
  background-color: #f5f5f5; 
}

#projectstatus tr:nth-of-type(odd):hover {
  background-color: #e5e5e5; 
}

#projectstatus tr:nth-of-type(even) {
  background-color: white; 
}

#projectstatus tr:nth-of-type(even):hover {
  background-color: #e5e5e5; 
}

.bigtable tr {
  border:1px solid #dcdcdc;
}

#search-box {
  -moz-appearance: textfield;
  -webkit-appearance: textfield;
  border: none;
  border-radius: 5em;
  box-shadow: inset 1px 2px 3px rgba(0,0,0,0.3);
  -moz-box-sizing: border-box;
  box-sizing: border-box;
  color: #333;
  font-family: inherit;
  font-size: 14px;
  height: 1.71428571428571em;
  line-height: 1.71428571428571;
  padding-left: 20px;
  position: static;
  font-size: 16px;
  padding: 5px 10px;
  background-image: none;
  margin: 7px;
}

.top-sticker, .noedge {
  top: 43px;
  left: 0px;
  font-size: 14px;
}

/* left navigation */

#left-top-nav {
  border-left: none; 
}

/* side panel  */

td.pane-header {
  border: 1px #bbb solid;
  border-right: none;
  border-left: none;
  background-color: #369;
  font-weight: bold;
  font-size: 12px;
  color: #ffffff;
  min-height: 24px;
  -moz-border-radius-topleft: 3px;
  border-top-left-radius: 3px;
  -moz-border-radius-topright: 3px;
  border-top-right-radius: 3px;
  border: 1px solid #ddd;
  padding: 4px 64px 4px 10px;
  line-height: 1.666666666667;
}

.pane-header a:link, .pane-header a:visited {
  color:#FFFFFF; 
  text-decoration: none;
}

#side-panel {
  background-color: #fff; 
}

#side-panel > div:not(#navigation) {
  display: none; 
}

#side-panel .task a {
  text-decoration: none;
  font-size: 12px;
  width: 10%; 
}
  
#side-panel .task a + a {
  width: 83%;
  padding: 4px; 
}
  
#side-panel .task a + a:hover {
  background-color: #e6e6e6;
  text-decoration: none; 
}

table.progress-bar.red td.progress-bar-done {
  background-color: #3465a4;
}
      
table.progress-bar.red {
  border: 1px solid #3465a4;
}

td.progress-bar-done {
  background-color: #3465a4;
}

/* main panel  */

#view-message #description a img {
  padding-right: 4px;

}

#main-panel {
  background: #ffffff; 
}

#main-panel > h1 {
  font-size: 24px;
  font-weight: normal;
  line-height: 1.25;
  margin-top: 10px;
}

#main-table {
  border-top: 0;
  border-bottom: 0; 
}

#viewList td.active {
  border: solid 1px #bbb;
  padding: 0.5em;
  border-bottom: none;
  vertical-align:middle;
  background-color: rgb(240,240,240);
  font-weight: bold;
  white-space: nowrap;
}

#viewList {
  border: none;
  margin-bottom: 0px;
  margin-top: 20px;
  width: 100%;
  white-space: nowrap;
}

#viewList td.inactive a {
  background: #f2f2f2;
  background: -moz-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: -webkit-gradient(linear,left top,left 
bottom,color-stop(0%,#fff),color-stop(100%,#f2f2f2));
  background: -webkit-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: -o-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: -ms-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: linear-gradient(top,#fff 0,#f2f2f2 100%);
  border-color: #ccc;
  border-width: 1px;
  color: #333;
  display: inline-block;
  margin: 0;
  padding: 10px 10px;
  text-decoration: none;
  text-shadow: 0 1px 0 white;
  vertical-align: baseline;
  height: auto;
  text-indent: 0;
  width: auto;
  float: left;
}

#viewList td.inactive a:hover {
  border-color: #000000;
}

#viewList td.active {
  border-bottom: none;
  vertical-align: middle;
  font-weight: bold;
  white-space: nowrap;
  background: #f2f2f2;
  background: -moz-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: -webkit-gradient(linear,left top,left 
bottom,color-stop(0%,#fff),color-stop(100%,#f2f2f2));
  background: -webkit-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: -o-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: -ms-linear-gradient(top,#fff 0,#f2f2f2 100%);
  background: linear-gradient(top,#fff 0,#f2f2f2 100%);
  border-color: #ccc;
  border-width: 1px;
  color: #333;
  margin: 0;
  padding: 10px 10px;
  text-decoration: none;
  text-shadow: 0 1px 0 white;
  height: auto;
  text-indent: 0;
  width: auto;
}

/* footer panel  */

#footer {
  border-top: 0 none;
  text-align: center;
  background: #f5f5f5;
}

input[name='j_username'], input[name='j_password'] {
    -moz-box-sizing: border-box;
    border: 1px solid #CCCCCC;
    border-radius: 3.01px 3.01px 3.01px 3.01px;
    box-shadow: 0 1px 3px #CCCCCC inset;
    color: #333333;
    font-size: inherit;
    margin: 0;
    max-width: 250px;
    vertical-align: baseline;
    width: 100%;
    height: 1.7em;
    line-height: 1.42857;
    padding: 4px 5px;
}

#yui-gen1-button {
    -moz-box-sizing: border-box;
    background: -moz-linear-gradient(center top , #FFFFFF 0px, #F2F2F2 
100%) repeat scroll 0 0 rgba(0, 0, 0, 0);
    border-radius: 3.01px 3.01px 3.01px 3.01px;
    color: #333333;
    cursor: pointer;
    display: inline-block;
    font-family: inherit;
    font-size: 14px;
    font-variant: normal;
    font-weight: normal;
    height: 2.14286em;
    line-height: 1.42857;
    margin: 0;
    padding: 4px 10px;
    text-decoration: none;
    text-shadow: 0 1px 0 #FFFFFF;
    vertical-align: baseline;
    white-space: nowrap;
    text-transform: capitalize;
}


#footer a:link, #footer a:visited {
  color:#707070; 
}

/* Console output */ 
body>pre,#main-panel>pre {
    font-size:14px;
    background-color:#393939;
    color:#b5c4d0;
    padding:20px 20px 30px;
    border-radius:3px;
    /*box-shadow*/
    -webkit-box-shadow: 0 1px 10px rgba(0, 0, 0, 0.32);
    -moz-box-shadow: 0 1px 10px rgba(0, 0, 0, 0.32);
    box-shadow: 0 1px 10px rgba(0, 0, 0, 0.32);
    /*background-clip*/
    -webkit-background-clip: padding-box;
    -moz-background-clip: /*@@prefixmycss->No equivalent*/; 
    background-clip:padding-box;
    /*@@prefixmycss->No equivalent*/
    : ;
    /*border-radius*/
    -webkit-border-radius: 5px;
    -moz-border-radius: 5px;
    border-radius: 5px;
    border: 1px solid rgba(0, 0, 0, 0.2);
    word-wrap: break-word;
    max-width: 1200px;
}

body>pre a,body>pre a:visited,#main-panel pre a,#main-panel pre a:visited {
    color:#9a8eb8;
}

/* Dooney */

.doony-callout-info {
  background-color: #f0f7fd;
  border-color: #d0e3f0;
}

.doony-downstream-link {
  display: block;
}

.doony-circle {
  border-radius: 50%;
}

.doony-circle-aborted {
  background: #999;
  background-image: -moz-radial-gradient(3px 3px 45deg, circle cover, 
#cccccc 0%, #999999 100%);
  background-image: -webkit-radial-gradient(3px 3px, circle cover, #cccccc, 
#999999);
  background-image: radial-gradient(circle at 3px 3px, #cccccc 0%, #999999 
100%);
}

.doony-circle-failure {
  background: #ac2925;
  background-image: -moz-radial-gradient(3px 3px 45deg, circle cover, 
#d9534f 0%, #ac2925 100%);
  background-image: -webkit-radial-gradient(3px 3px, circle cover, #d9534f, 
#ac2925);
  background-image: radial-gradient(circle at 3px 3px, #d9534f 0%, #ac2925 
100%);
}

.doony-circle-success {
  background: #397439;
  background-image: -moz-radial-gradient(3px 3px 45deg, circle cover, 
#72d472 0%, #397439 100%);
  background-image: -webkit-radial-gradient(3px 3px, circle cover, #72d472, 
#397439);
  background-image: radial-gradient(circle at 3px 3px, #72d472 0%, #397439 
100%);
}

.doony-circle-warning {
  background: #f0ad4e;
  background-image: -moz-radial-gradient(3px 3px 45deg, circle cover, 
#f0ad4e 0%, #d58512 100%);
  background-image: -webkit-radial-gradient(3px 3px, circle cover, #f0ad4e, 
#d58512);
  background-image: radial-gradient(circle at 3px 3px, #f0ad4e 0%, #d58512 
100%);
}


plugins:
I updated these plugins after the upgrade (the versions below are the 
versions prior to the upgrade):
Jenkins Mailer Plugin
SSH Credentials Plugin
External Monitor Job Type Plugin
Jenkins SSH Slaves plugin
Maven Integration plugin
Credentials Plugin

active-directory1.33falsefalseant1.2falsetrueantisamy-markup-formatter1.1
truefalseanything-goes-formatter1.0truefalseartifactdeployer0.28falsefalse
artifactory2.2.1truefalsebranch-api0.2-beta-1truefalsebuild-name-setter1.3
truefalsebuild-pipeline-plugin1.4.3truefalsebuild-timeout1.12.2truefalse
buildtriggerbadge1.2truefalseclone-workspace-scm0.6falsefalse
conditional-buildstep1.3.3truefalseconfig-file-provider2.7.1truefalse
configurationslicing1.38.3truefalseconsole-column-plugin1.5falsefalse
copyartifact1.28truefalsecredentials1.9.4truetruecvs2.11falsetrue
delivery-pipeline-plugin0.8.6truefalsedeploy1.9truefalsedescription-setter
1.8truefalsedynamicparameter0.2.0truefalseemail-ext2.38.1truefalseenvinject
1.89truefalseextended-read-permission1.0truefalseexternal-monitor-job1.2
falsetruegit2.0truefalsegit-client1.4.6truefalsegit-server1.2truefalse
gitlab-hook1.0.0truefalsegroovy1.14truefalsegroovy-postbuild1.8truefalseivy
1.23.2falsefalsejavadoc1.1truetruejenkins-pipeline-plugin1.0.34-10truefalse
job-dsl1.21truefalsejob-node-stalker1.0.3truefalsejobConfigHistory2.5false
falsejoin1.15truefalsejquery1.7.2-1truefalsejquery-ui1.0.2truefalsejunit
1.2-beta-4truefalselastsuccessdescriptioncolumn1.0truefalseldap1.7truetrue
literate0.2-beta-1truefalsemailer1.8truetruemanaged-scripts1.1.1truefalse
matrix-auth1.1truetruematrix-project1.4.1truefalsemaven-plugin2.1truetrue
maven-repo-cleaner1.2truefalsemsbuild1.21truefalsemstest0.7truefalse
mstestrunner1.0.1truefalsenant1.4.3falsefalsenested-view1.14falsefalse
next-build-number1.1truefalsepam-auth1.1truetrueparameterized-trigger2.21
truefalseperiodicbackup1.3falsefalsepostbuildscript0.16truefalse
project-inheritance1.4.12falsefalsepromoted-builds2.14truefalseredmine0.15
truefalserepository1.0falsefalserole-strategy2.1.0truefalseruby-runtime0.12
truefalserun-condition1.0truefalsescm-api0.2truefalsescript-security1.13true
falsescriptler2.6.1truefalsesectioned-view1.18falsefalsesimple-theme-plugin
0.3truefalsesonar2.1truefalsessh2.3truefalsessh-credentials1.6truetrue
ssh-slaves1.5truetruesubversion2.0-beta-1truetruetimestamper1.5.7truefalse
token-macro1.10truefalsetranslation1.10falsetruewindows-slaves1.0truefalse
ws-cleanup0.19falsefalsexvnc1.14truefalse

Thanks,
Xavier


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