weinre is shipped as two archives available at https://github.com/phonegap/weinre/archives/master

• weinre-jar-x.y.z.zip
  This archive includes a Java .jar file.
• weinre-mac-x.y.z.zip
  This archive includes a Mac OS X application.

Install the .jar and/or Mac OS X application wherever you wish. At runtime, the .jar file is not sensive to the directory it is installed in, or the current directory when it's launched.