Hm, well, I added that file to the classpath (and that class in present in that file) and things moved further, but still an error, I get a feeling, something is not set right 'globally'... I did not have such issues, when setting IntelliJ up the first time I went through this...

Once again, here is the Configuration for the 'Labkey Dev' Run:

Main class: org.apache.catalina.startup.Bootstrap
VM options:
-ea
-Xmx1G
-XX:MaxPermSize=512M
-Dsun.io.useCanonCaches=false
-Djava.endorsed.dirs="/usr/local/tomcat/common/endorsed"
-classpath
"/usr/local/tomcat/bin/bootstrap.jar:/usr/local/tomcat/lib/catalina.jar:/usr/local/tomcat/lib/tomcat-coyote.jar:/usr/lib/jvm/java-7-oracle/lib/tools.jar:/home/ldashevs/Labkey/idea-IU-117.117/lib/idea_rt.jar:./bin/tomcat-juli.jar"
-Dcatalina.base="/usr/local/tomcat/"
-Dcatalina.home="/usr/local/tomcat/"
-Djava.io.tmpdir="/usr/local/tomcat/temp"
-Ddevmode=true

Program arguments: start
Working directory: /usr/local/tomcat
Environment variables: <blank>
Use classpath of module: LabKey
unchecked: Use alternative JRE
unchecked: Enable capturing from snapshots

Before launch
checked: Make
unchecked: 4 other checkboxes


Anything else I'm missing?


Error:

/usr/lib/jvm/java-7-oracle/bin/java -agentlib:jdwp=transport=dt_socket,address=127.0.0.1:41194,suspend=y,server=n -ea -Xmx1G -XX:MaxPermSize=512M -Dsun.io.useCanonCaches=false -Djava.endorsed.dirs=/usr/local/tomcat/common/endorsed -classpath /usr/local/tomcat/bin/bootstrap.jar:/usr/local/tomcat/lib/catalina.jar:/usr/local/tomcat/lib/tomcat-coyote.jar:/usr/lib/jvm/java-7-oracle/lib/tools.jar:/home/ldashevs/Labkey/idea-IU-117.117/lib/idea_rt.jar:./bin/tomcat-juli.jar -Dcatalina.base=/usr/local/tomcat/ -Dcatalina.home=/usr/local/tomcat/ -Djava.io.tmpdir=/usr/local/tomcat/temp -Ddevmode=true -javaagent:/home/ldashevs/Labkey/idea-IU-117.117/plugins/Groovy/lib/agent/gragent.jar -Dfile.encoding=UTF-8 org.apache.catalina.startup.Bootstrap start
Connected to the target VM, address: '127.0.0.1:41194', transport: 'socket'
Aug 26, 2013 6:09:13 PM org.apache.catalina.core.AprLifecycleListener init
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /home/ldashevs/Labkey/idea-IU-117.117/bin:/home/ldashevs/Programs/j3d/lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Aug 26, 2013 6:09:13 PM org.apache.tomcat.util.digester.Digester startElement
SEVERE: Begin event threw error
java.lang.NoClassDefFoundError: javax/servlet/http/HttpServletRequest
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:791)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
    at java.lang.Class.getDeclaredMethods0(Native Method)
    at java.lang.Class.privateGetDeclaredMethods(Class.java:2451)
    at java.lang.Class.privateGetPublicMethods(Class.java:2571)
    at java.lang.Class.getMethods(Class.java:1429)
    at org.apache.tomcat.util.IntrospectionUtils.findMethods(IntrospectionUtils.java:841)
    at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:271)
    at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:262)
    at org.apache.catalina.startup.SetAllPropertiesRule.begin(SetAllPropertiesRule.java:66)
    at org.apache.tomcat.util.digester.Digester.startElement(Digester.java:1356)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:506)
    at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:182)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1303)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2717)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:607)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:489)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:835)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:123)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1210)
    at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:568)
    at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1642)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:524)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:562)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:261)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:413)
Caused by: java.lang.ClassNotFoundException: javax.servlet.http.HttpServletRequest
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
    ... 41 more

java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:601)
    at org.apache.catalina.startup.Bootstrap.load(Bootstrap.java:261)
    at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:413)
Caused by: java.lang.NoClassDefFoundError: javax/servlet/http/HttpServletRequest
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:791)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
    at java.lang.Class.getDeclaredMethods0(Native Method)
    at java.lang.Class.privateGetDeclaredMethods(Class.java:2451)
    at java.lang.Class.privateGetPublicMethods(Class.java:2571)
    at java.lang.Class.getMethods(Class.java:1429)
    at org.apache.tomcat.util.IntrospectionUtils.findMethods(IntrospectionUtils.java:841)
    at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:271)
    at org.apache.tomcat.util.IntrospectionUtils.setProperty(IntrospectionUtils.java:262)
    at org.apache.catalina.startup.SetAllPropertiesRule.begin(SetAllPropertiesRule.java:66)
    at org.apache.tomcat.util.digester.Digester.startElement(Digester.java:1356)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:506)
    at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:182)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1303)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2717)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:607)
    at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:489)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:835)
    at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764)
    at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:123)
    at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1210)
    at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:568)
    at org.apache.tomcat.util.digester.Digester.parse(Digester.java:1642)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:524)
    at org.apache.catalina.startup.Catalina.load(Catalina.java:562)
    ... 6 more
Caused by: java.lang.ClassNotFoundException: javax.servlet.http.HttpServletRequest
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
    ... 41 more
Disconnected from the target VM, address: '127.0.0.1:41194', transport: 'socket'

Process finished with exit code 0