Hi All!
I’m newbie here, all because my xwiki installation was running absolutely problem-free for more than 2 years 
But I have touched the working stuff, by making stupid desicion to update the system: as a result, xwiki initialization fails at about 30% and navigation tree is not visible anymore.
My setup: Ubuntu 16 LTS, tomcat8
Updated the following:
Blockquote WIKI Package vim-common updated from 2:7.4.1689-3ubuntu1.2 to 2:7.4.1689-3ubuntu1.3
WIKI Package vim-runtime updated from 2:7.4.1689-3ubuntu1.2 to 2:7.4.1689-3ubuntu1.3
WIKI Package vim-tiny updated from 2:7.4.1689-3ubuntu1.2 to 2:7.4.1689-3ubuntu1.3
WIKI Package btrfs-tools updated from 4.4-1ubuntu1 to 4.4-1ubuntu1.1
WIKI Package bzip2 updated from 1.0.6-8 to 1.0.6-8ubuntu0.2
WIKI Package libexpat1 updated from 2.1.0-7ubuntu0.16.04.3 to 2.1.0-7ubuntu0.16.04.5
WIKI Package libfreetype6 updated from 2.6.1-0.1ubuntu2.3 to 2.6.1-0.1ubuntu2.4
WIKI Package psmisc updated from 22.21-2.1build1 to 22.21-2.1ubuntu0.1
WIKI Package vim updated from 2:7.4.1689-3ubuntu1.2 to 2:7.4.1689-3ubuntu1.3
WIKI Package dbus updated from 1.10.6-1ubuntu3.3 to 1.10.6-1ubuntu3.4
WIKI Package dh-python updated from 2.20151103ubuntu1.1 to 2.20151103ubuntu1.2
WIKI Package libbz2-1.0 updated from 1.0.6-8 to 1.0.6-8ubuntu0.2
WIKI Package libdbus-1-3 updated from 1.10.6-1ubuntu3.3 to 1.10.6-1ubuntu3.4
Looked at tomcat startup log:
Blockquote Sep 18, 2019 10:19:14 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common/classes], exists: [false], isDirectory: [false], canRead: [false]
Sep 18, 2019 10:19:14 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/common], exists: [false], isDirectory: [false], canRead: [false]
Sep 18, 2019 10:19:14 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server/classes], exists: [false], isDirectory: [false], canRead: [false]
Sep 18, 2019 10:19:14 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/server], exists: [false], isDirectory: [false], canRead: [false]
Sep 18, 2019 10:19:14 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared/classes], exists: [false], isDirectory: [false], canRead: [false]
Sep 18, 2019 10:19:14 AM org.apache.catalina.startup.ClassLoaderFactory validateFile
WARNING: Problem with directory [/usr/share/tomcat8/shared], exists: [false], isDirectory: [false], canRead: [false]
Sep 18, 2019 10:19:15 AM org.apache.catalina.startup.VersionLoggerListener log
INFO: Server version: Apache Tomcat/8.0.32 (Ubuntu)
…
Next series of warings:
Blockquote INFO: Starting Servlet Engine: Apache Tomcat/8.0.32 (Ubuntu)
Sep 18, 2019 10:19:15 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deploying configuration descriptor /etc/tomcat8/Catalina/localhost/xwiki.xml
2019-09-18 10:19:20,830 [localhost-startStop-1] INFO iPropertiesConfigurationSource - loading xwiki.properties from default location /etc/xwiki/xwiki.properties
2019-09-18 10:19:20,987 [localhost-startStop-1] INFO o.x.e.i.ServletEnvironment - Using permanent directory [/var/lib/xwiki/data]
2019-09-18 10:19:24,735 [localhost-startStop-1] WARN ltInstalledExtensionRepository - Invalid extension [org.xwiki.contrib:flavor-demo/1.0.1] on namespace [wiki:xwiki] (InvalidExtensionException: Dependency [org.xwiki.platform:xwiki-platform-oldcore-[9.8.1]] is incompatible with the core extension [org.xwiki.platform:xwiki-platform-legacy-oldcore/11.7])
2019-09-18 10:19:26,969 [localhost-startStop-1] INFO o.x.s.f.i.FilesystemStoreTools - Using filesystem store directory [/var/lib/xwiki/data/store/file]
2019-09-18 10:19:27,187 [localhost-startStop-1] INFO o.x.s.s.i.EmbeddedSolrInstance - Starting embedded Solr server…
2019-09-18 10:19:27,187 [localhost-startStop-1] INFO o.x.s.s.i.EmbeddedSolrInstance - Using Solr home directory: [/var/lib/xwiki/data/solr]
2019-09-18 10:19:28,274 [localhost-startStop-1] WARN o.e.j.u.s.S.config - No Client EndPointIdentificationAlgorithm configured for SslContextFactory@3c059899[provider=null,keyStore=null,trustStore=null]
2019-09-18 10:19:28,492 [localhost-startStop-1] WARN o.e.j.u.s.S.config - No Client EndPointIdentificationAlgorithm configured for SslContextFactory@5f387f92[provider=null,keyStore=null,trustStore=null]
2019-09-18 10:19:29,081 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrConfig - solrconfig.xml: of 2048 is greater than global limit of 1024 and will have no effect
2019-09-18 10:19:29,081 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrConfig - set ‘maxBooleanClauses’ in solr.xml to increase global limit
2019-09-18 10:19:29,274 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrResourceLoader - Solr loaded a deprecated plugin/analysis class [solr.TrieIntField]. Please consult documentation how to replace it accordingly.
2019-09-18 10:19:29,280 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrResourceLoader - Solr loaded a deprecated plugin/analysis class [solr.TrieFloatField]. Please consult documentation how to replace it accordingly.
2019-09-18 10:19:29,286 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrResourceLoader - Solr loaded a deprecated plugin/analysis class [solr.TrieLongField]. Please consult documentation how to replace it accordingly.
2019-09-18 10:19:29,290 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrResourceLoader - Solr loaded a deprecated plugin/analysis class [solr.TrieDoubleField]. Please consult documentation how to replace it accordingly.
2019-09-18 10:19:29,297 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrResourceLoader - Solr loaded a deprecated plugin/analysis class [solr.TrieDateField]. Please consult documentation how to replace it accordingly.
2019-09-18 10:19:29,322 [coreLoadExecutor-9-thread-1] WARN o.a.s.s.FieldTypePluginLoader - TokenizerFactory is using deprecated 6.4.2 emulation. You should at some point declare and reindex to at least 7.0, because 6.x emulation is deprecated and will be removed in 8.0
2019-09-18 10:19:29,327 [coreLoadExecutor-9-thread-1] WARN o.a.s.s.FieldTypePluginLoader - TokenizerFactory is using deprecated 6.4.2 emulation. You should at some point declare and reindex to at least 7.0, because 6.x emulation is deprecated and will be removed in 8.0
2019-09-18 10:19:29,328 [coreLoadExecutor-9-thread-1] WARN o.a.s.s.FieldTypePluginLoader - TokenFilterFactory is using deprecated 6.4.2 emulation. You should at some point declare and reindex to at least 7.0, because 6.x emulation is deprecated and will be removed in 8.0
2019-09-18 10:19:29,332 [coreLoadExecutor-9-thread-1] WARN o.a.s.s.FieldTypePluginLoader - TokenFilterFactory is using deprecated 6.4.2 emulation. You should at some point declare and reindex to at least 7.0, because 6.x emulation is deprecated and will be removed in 8.0
2019-09-18 10:19:29,332 [coreLoadExecutor-9-thread-1] WARN o.a.s.c.SolrResourceLoader - Solr loaded a deprecated plugin/analysis class [solr.SynonymFilterFactory]. Please consult documentation how to replace it accordingly.
2019-09-18 10:19:29,333 [coreLoadExecutor-9-thread-1] WARN o.a.s.s.FieldTypePluginLoader - TokenFilterFactory is using deprecated 6.4.2 emulation. You should at some point declare and reindex to at least 7.0, because 6.x emulation is deprecated and will be removed in 8.0
… + lots and lots of warnings about deprecated items, about 300 rows
Next thing:
Blockquote 2019-09-18 10:19:30,756 [localhost-startStop-1] ERROR .o.i.DefaultObservationManager - Failed to lookup listeners
org.xwiki.component.manager.ComponentLookupException: Failed to lookup component with type [interface org.xwiki.observation.EventListener] and hint [solr.availablelocales]
… bla-bla-bla …
Caused by: org.xwiki.component.manager.ComponentLookupException: Failed to lookup component [org.xwiki.search.solr.internal.SolrInstanceProvider] identified by type [javax.inject.Provider<org.xwiki.search.solr.internal.api.SolrInstance>] and hint [default]
Caused by: org.xwiki.component.phase.InitializationException: Failed to lookup configured Solr instance type [embedded]
Caused by: org.xwiki.component.manager.ComponentLookupException: Failed to lookup component [org.xwiki.search.solr.internal.EmbeddedSolrInstance] identified by type [interface org.xwiki.search.solr.internal.api.SolrInstance] and hint [embedded]
Caused by: org.xwiki.component.phase.InitializationException: Failed to initialize the Solr embedded server with home directory set to [/var/lib/xwiki/data/solr]
Caused by: org.apache.solr.client.solrj.SolrServerException: Failed to initialize the Solr core. Please check the configuration and log messages.
…
2019-09-18 10:19:30,937 [Finalizer] ERROR o.a.s.u.SolrIndexWriter - SolrIndexWriter was not closed prior to finalize(), indicates a bug – POSSIBLE RESOURCE LEAK!!!
2019-09-18 10:19:30,940 [Finalizer] ERROR o.a.s.u.SolrIndexWriter - Error closing IndexWriter
java.lang.NullPointerException: null
… at bla-bla-bla …
And finishing startup with:
Blockquote Sep 18, 2019 10:19:31 AM org.apache.catalina.startup.HostConfig deployDescriptor
INFO: Deployment of configuration descriptor /etc/tomcat8/Catalina/localhost/xwiki.xml has finished in 15,802 ms
Sep 18, 2019 10:19:31 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /var/lib/tomcat8/webapps/ROOT
Sep 18, 2019 10:19:31 AM org.apache.jasper.servlet.TldScanner scanJars
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
Sep 18, 2019 10:19:31 AM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /var/lib/tomcat8/webapps/ROOT has finished in 264 ms
Sep 18, 2019 10:19:31 AM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler [“http-nio-8080”]
Sep 18, 2019 10:19:31 AM org.apache.catalina.startup.Catalina start
INFO: Server startup in 16121 ms
For me it looks like solr engine refuses to start because of [solr.availablelocales] problem. Any thoughts and help how to correct this would be much appreciated.