The upgrade process for the webapp distribution (described in readme.txt) suggests that the distribution be unpacked in the same directory as the old JIRA install. The webapp/ directory will then be overwritten, and when 'ant war' is run, the customized files in edit-webapp/ are copied over webapp/.

This is not safe, since unused files from old versions (specifically old jars) can cause conflicts in the new version.

Solutions, in order of preference:

1) JIRA webapp root directory should be 'jira-<version>' instead of just 'webapp'. Then, if the user unpacks to c:\jira, after a few versions one would have:

c:\jira\jira-1.4
c:\jira\jira-2.0.2
c:\jira\jira-2.1
c:\jira\edit-webapp

With edit-webapp/ contents overwriting each one in the usual manner.

2) Edit the docs to describe an equivalent process: unpack to a separate directory, then copy across one's edit-webapp/ directory.

--Jeff