We could always try to hack the new format and make our own compile tools before the test ends, but I am too lazy.
Anyway, someone I know made a legal tool to mod Source maps. I shared the data with him I found with him from a thread here. I turns ot there is a pointer in the file to the entity lump and the size next to that. I told him he should make his software move the entity lump to the end of the file.
You can get it here->
http://www.geocities.com/sysys/ented/
Also works with HL1.
Anyway, if you decide you DO want to hack the HL2 BSP format, you can get help here ->
http://forums.qhimm.com
There are some talented hackers there. And by hackers, I mean guru coders who can decipher file formats.