I'd like to suggest that a command line argument be added to BuildTools to control where a copy of the output files is placed once BuildTools finishes running. There could be a different argument for the Bukkit API, the Spigot API, the CraftBukkit server, and the Spigot server.

Example:
java -jar BuildTools.jar --spigotapi ./globaltarget/spigot-api.jar
java -jar BuildTools.jar --cbserver ./globaltarget/craftbukkit-server.jar
java -jar BuildTools.jar --spigotserver ./globaltarget/spigot-server.jar --cbapi ./globaltarget/craftbukkit-api.jar

This would be useful in scripts that need to get the version that was just built and then do something with it (ie. push it to new servers on a dedi or update several plugins' development environments). Since BuildTools places the version number after the name of the jar file in each build, it is very difficult to have even Bash scripts get the correct jar file. These arguments put it in a specific place with a specific name that doesn't depend on version numbers.

My BuildTools version is git-BuildTools-e9ee0aa-38. The version argument to create an issue wouldn't accept the BuildTools version, so I had to put a Spigot version in instead.