The source code in the FieldTrip toolbox is split over multiple directories reflecting the modular organization. The modular organization facilitates a separation between end-user functions that also do data bookkeeping, and low level functions that focus on the algorithms.
For keeping track of new ideas, feature requests and bugs, we use bugzilla. We have a seperate page here on the wiki where some of the known problems with the documentation are listed.
For many of the tools (github, wiki, mailman, twitter, facebook) that we use we have made an integration, e.g. an update on the wiki is automatically tweeted.