instead of having $root/models $root/tokens etc, it should be something like

$root/core/models
$root/core/tokens
(for things distributed with engine)

$root/(thirpartyname)/models
$root/(thirpartyname)/tokens
(for hak-pak like downloads)

$root/(campaignname)/models
$root/(campaignname)/tokens
(for things distributed with given campaign, stuff autodownloaded from server would go here probably)

$root/local/models
$root/local/tokens
(for final local installation)

Precedence would be take by 'local' dir, then campaign dir, third party dirs (order as specified in campaign ruleset??) and at very last core dir.

Core dir could be always nuked and unpacked from original - no new stuff go there.
Runtime file can go to
$root/vmat.cfg
$root/logs/log1.log
$root/autoexec.macro

Have to change inside engine to refer to resources as model/bugbear.mdl instead of just bugbear.mdl (so only main paths of each module would go to asset loader, not each of the subpaths).