The link is still there and it points to the right spot, but the actual file in include/mk is gone. I installed the 
service pack with the -E on sudo as well. I don't have my laptop with me but I'll post my env vars the next chance I get
. 

I tried compiling the BSP (beagle bone) without the service pack and it worked fine. I could back that folder up and 
install the service pack but I have no idea what else might be breaking...

> Is /opt/qnx650/target/qnx6/usr/include/qconfig.mk missing?
> 
> 
> It should be a link to mk/qconf-linux.mk
> 
> Also check you env vars;
> 
> QNX_HOST
> QNX_TARGET
> MAKEFLAGS
> PATH
> 
> 
> Sent from my BB 
> 
> ----- Original Message -----
> From: Jon Wallace [mailto:community-noreply@qnx.com]
> Sent: Saturday, November 24, 2012 04:15 AM
> To: momenticsgs-community <momenticsgs-community@community.qnx.com>
> Subject: qconfig.mk file disappears after installing the 6.5 service pack
> 
> 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!
> 
> 
> 
> 
> _______________________________________________
> 
> QNX Momentics Getting Started
> http://community.qnx.com/sf/go/post97432
> To cancel your subscription to this discussion, please e-mail momenticsgs-
> community-unsubscribe@community.qnx.com

QNX_TARGET=/opt/qnx650/target/qnx6

QNX_HOST=/opt/qnx650/host/linux/x86

PATH=/usr/lib/lightdm/lightdm:
/usr/local/sbin:
/usr/local/bin:
/usr/sbin:
/usr/bin:
/sbin:
/bin:
/usr/games:
/opt/qnx650/host/linux/x86/usr/bin:
/etc/qnx/bin


MAKEFLAGS=-I/opt/qnx650/target/qnx6/usr/include

I don't know for sure, but these all look good to me

I am having the exact same problem and I did install sp1 using the -E option but it did not help. I still have this 
issue :(

I seriously think it is a bug, it happens to me to, under ubuntu 12.04.