Take a look, for example, at http://www.atlassian.com/software/jira/docs/v3.12/install-war.html .

In there, it refers to instructions in README.txt, which only talks about the standalone deployment.

Follow from install-war.html to http://www.atlassian.com/software/jira/docs/v3.12/config_overview.html .

The file layout in there isn't even accurate. FTR, the current unpacked 3.12.2 directories look like:
[wyliek@fodevsx4:/proj/fotech-build/wyliek/p4/fotech/shared/jira]$ ll atlassian-jira-enterprise-3.12.2-standalone/
total 64
rw-rw--- 1 wyliek fodev 688 Feb 11 23:02 NOTICE
rw-rw--- 1 wyliek fodev 3024 Feb 11 22:39 README.html
rw-rw--- 1 wyliek fodev 1952 Feb 11 22:39 README.txt
drwxrws--x 13 wyliek fodev 4096 Apr 18 16:37 atlassian-jira/
drwxrws--x 2 wyliek fodev 4096 Apr 18 16:37 bin/
drwxrws--x 6 wyliek fodev 4096 Apr 18 16:37 common/
drwxrws--x 3 wyliek fodev 4096 Apr 18 16:37 conf/
drwxrws--x 2 wyliek fodev 4096 Apr 18 16:37 external-source/
drwxrws--x 2 wyliek fodev 4096 Apr 18 16:37 licenses/
drwxrws--x 2 wyliek fodev 4096 Feb 11 23:02 logs/
drwxrws--x 4 wyliek fodev 4096 Apr 18 16:37 server/
drwxrws--x 4 wyliek fodev 4096 Apr 18 16:37 shared/
drwxrws--x 2 wyliek fodev 4096 Apr 18 16:37 temp/
drwxrws--x 2 wyliek fodev 4096 Apr 18 16:37 tomcat-docs/
drwxrws--x 2 wyliek fodev 4096 Feb 11 23:02 webapps/
drwxrws--x 2 wyliek fodev 4096 Feb 11 23:02 work/

Note the lack of build.xml and the fact that the docs don't accurately state what this directory should look like at all.