Science Collaboration Framework repository structure
SCF may have to move to a full Drupal distribution at some point, but for now it is a profiles directory that can be put into any Drupal 6 installation (before or after install is run).
Modules
The modules directory is currently broken down into categories.
modified
If a module is customized, modifications to a module that is available elsewhere, it should be called something else. Otherwise there are namespace conflicts, one overriding the other, and potentially breaking the dependencies for it.
When the modification is the application of a patch, whether written by yourself or others, that is supposed to be nondestructive (ie, going back into a drupal.org module without breaking anyone's site), there it should not be renamed. For instance the only modules currently in "modified" are gopubmed (which I ported to Drupal 6 and sent that code back) and taxonomy_xml (where i'm adding an obo import option and getting it contributed back).
Being in modified should be a temporary state to get around lag time in changes being committed to CVS by other maintainers. If changes are not going to be committed back to the original module project hosted on Drupal.org, another approach must be taken.
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