I'm just getting my environment set up for the first time, I'm completely new to QnX but I've been really impressed with
 the level of documentation so far. There's one roadblock that I haven't been able to find an answer to by searching QnX
, Foundry, or the whole internet: I can't build my bsp because the make system can't find qconfig.mk. I checked out my /
opt/qnx650/target/qnx6/usr/include/mk directory and this is what I see:

jon@jon-netbook:/opt/qnx650/target/qnx6/usr/include/mk$ ls
nto_mips.mk

Clearly there should be a lot more. So I uninstalled the SDP and re-installed (I used sudo -E on the package this time, 
I left out the E flag the first time and I thought I might as well try that) Well after doing that, I checked the target
 include files again and lo and behold:

jon@jon-netbook:/opt/qnx650/target/qnx6/usr/include/mk$ ls
ab.mk            makepriv-qnx   ntoxdev.mk      qconf-nto.mk    qrules.mk
build-cfg        makepriv-unix  os_linux.mk     qconf-win32.mk  qtargets.mk
buildlist.mk     nto_arm.mk     os_nto.mk       qdepfile.mk     recurse.mk
flist-unix       nto_mips.mk    os_win32.mk     qlevel.mk
flist-win32      nto_ppc.mk     phapps.mk       qmacros.mk
linux_x86.mk     nto_sh.mk      prod_utils.mk   qmake-cfg.mk
makepriv-nt.bat  nto_x86.mk     qconf-linux.mk  qphabtarg.mk

At this point I thought I was in the clear so I installed the service pack and went to build my bsp again and I got the 
same error! No qconfig.mk. So I went back the the includes directory and it was back to the way it was the first time. 
It seems like the service pack installer is clobbering that folder on my host. Has anyone seen this before?

Here's the file names for each installer, they look like they have build dates/numbers so I'm hoping its helpful

Main:
qnxsdp-6.5.0-201007091524-linux.bin
Service Pack:
qnxsdp-6.5.0SP1-201206271006-linux.bin

My system:
Linux jon-netbook 3.2.0-33-generic-pae #52-Ubuntu SMP Thu Oct 18 16:39:21 UTC 2012 i686 i686 i386 GNU/Linux
Ubuntu 12.04 LTS

Thanks in advance!