per Scott, these include files can't standalone, but are getting compiled due to the .jsp suffix. Scott mentioned renaming them to .jsi to avoid this problem.

—
Buildfile: build.xml

init:

clean:
[delete] Deleting directory C:\Projects\jira-2.4.1\tmp\build
[delete] Deleting directory C:\Projects\jira-2.4.1\dist-generic
[delete] Deleting directory C:\Projects\jira-2.4.1\dist-tomcat
[delete] Deleting directory C:\Projects\jira-2.4.1\tmp

war:
[mkdir] Created dir: C:\Projects\jira-2.4.1\tmp\build\war
[mkdir] Created dir: C:\Projects\jira-2.4.1\dist-generic
[mkdir] Created dir: C:\Projects\jira-2.4.1\dist-tomcat
[copy] Copying 1396 files to C:\Projects\jira-2.4.1\tmp\build\war
[copy] Copied 2 empty directories to C:\Projects\jira-2.4.1\tmp\build\war
[copy] Copying 1 file to C:\Projects\jira-2.4.1\tmp\build\war
[jar] Building jar: C:\Projects\jira-2.4.1\dist-generic\atlassian-jira-2.4.1.war
[jar] Building jar: C:\Projects\jira-2.4.1\dist-tomcat\atlassian-jira-2.4.1.war
[copy] Copying 1 file to C:\Projects\jira-2.4.1\dist-tomcat
[echo]
[echo] --------------------------------------------------
[echo] Deployable WARs generated:
[echo]
[echo] TOMCAT: C:\Projects\jira-2.4.1\dist-tomcat\atlassian-jira-2.4.1.war
[echo] GENERIC: C:\Projects\jira-2.4.1\dist-generic\atlassian-jira-2.4.1.war
[echo]
[echo]
[echo] See http://www.atlassian.com/software/jira/docs/latest/servers/ for install instructions
[echo] --------------------------------------------------
[echo]

weblogic:
[mkdir] Created dir: C:\Projects\jira-2.4.1\weblogic
[unzip] Expanding: C:\Projects\jira-2.4.1\dist-generic\atlassian-jira-2.4.1.war into C:\Projects\jira-2.4.1\weblogic
[java] Error: [jspc]: 6 file(s) failed:
[java] /includes/js/savedfilters.jsp
[java] /includes/js/history.jsp
[java] /includes/dashboard/inprogressissues.jsp
[java] /includes/decorators/headerpopups.jsp
[java] /includes/decorators/bodytop.jsp
[java] /includes/dashboard/projects.jsp
[java] Errors encountered while compiling 'weblogic' :
<snip>