I also got Agent Analyst to work with ArcGIS 10.2 (at least so far). I had to perform the steps noted above, but given that it was a bit confusing with some of the responses I will summarize here:
Create Refresh.exe.config file with a text editor and save it along with Refresh.exe (typically in C:\Repast 3\Agent Analyst\Refresh). The Refresh.exe.config contents will be identical to the contents of the configuration file described here ("Update 2"): ArcGIS 10.1 using Repast's Agent Analyst Extension - refresh.exe does not work but you must replace newVersion="10.1.0.0" with newVersion="10.2.0.0".
As noted above, edit the agent_analyst.bat and agent_analyst_run.bat files in the installation folder (C:\Repast 3\Agent Analyst) so that the folder paths contain Desktop10.2 in the folder path strings:
rem set ARC_JAVA="C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\java"
rem set ARC_JAVAW="C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\javaw"
rem set ARCOBJECTS_JAR="C:\Program Files (x86)\ArcGIS\Desktop10.2\java\lib\arcobjects.jar"
Then, edit your Environment Variables to make sure that ARC_JAVA, ARC_JAVAW, and ARCOBJECTS_JAR have a fully specified path entered for each variable (like what is in the .bat files above).
Then, in my Environment Variables, I had to move ARC_JAVA (C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\java), ARC_JAVAW (C:\Program Files (x86)\ArcGIS\Desktop10.2\java\jre\bin\javaw), ARCOBJECTS_JAR (C:\Program Files (x86)\ArcGIS\Desktop10.2\java\lib\arcobjects.jar), AGENT_ANALYST (C:\Repast 3\Agent Analyst), and AGENT_ANALYST_VOL (C:) from my User Variables to my System Variables. Depending on your situation, I foresee that some people may not need to do this. If you install software and manage your system with a separate ADMIN account, then I think you will need to do this...I had to do so to get it to work.
Finally, make sure you restart your system and open a fresh ArcGIS session...
I'm new to Agent Analyst so I don't know if there will be other issues down the road, but now I am at least able to see the Agent Analyst user interface when adding a new tool so it appears that everything is working well so far.
refresh.config.exe
as noted above, orRefresh.exe.config
as named in blah238's answer? It should be the second one, and should be located in the same directory as refresh.exe