Didn't know about SCCM, although that certainly isn't the case here at least - we often go digging into the source directories!
Then again, maybe because the desktop.ini files might already exist it might not necessarily cause an issue on subsequent visits.
Well SCCM is a bit different as you have the files in the source directory and the packages in the distribution point. If you went mucking about with the DP then I guess that would mess things up, but the source directory is fine.
We're also looking to do the same or though I'd want to recreate the packages or app v. Are there any other tools anyone can suggest? Or does SCCM pretty much cover everything in terms of management?
Would this be come you RMMC?
There's no direct package building system in SCCM - it can handle deployment of EXE packages directly though if you so wish or standard MSI. You can continue to use something like winstallLE for original creation if need be, however there's very little software these days that isn't deployable via one standard method or another.
SCCM wouldn't entirely replace the RMMC - the latter is a mixture of AD and GPO, SCCM works alongside and with AD. A bit of a breakdown from RMMC to SCCM would be thus:
RMMC Functions (SCCM Equivelent)
User and computer account, groups, profiles etc (AD)
Software deployment of existing packages (SCCM console)
Software deployment groups (SCCM console via device or user collections)
Registry Policies (GPO/GPP)
There's little else that RMMC itself does anyway. To directly replace other functions from an RM network, you obviously can add AV management of System Center Endpoint Protection
Winstall LE capability is missing but you can use any standard MSI packager
System builds ala WOrkstation Build Manager/RMR via SCCM console directly