I've gotten this question a lot recently and so thought to share my thinking on the subject.
We here in the TDI team use RTC for shared projects. Due to technical difficulties getting TDI and RTC to run in the same Eclipse environment, I run them separately: TDI in my Windows image (Parallels) and RTC under OS X.
First step is to set up a workspace for RTC, which I call imaginatively enough 'workspace_RTC'. Here I copy in the project that I created locally - at least for projects where I do the initial development.
From RTC I import the project that was copied to the workspace_RTC directory. Only the AssemblyLines and Resources folders (and contents) are tagged as included in source management. Furthermore, under Resource > Properties you will only want to include the actual Property Stores designed for this solution.
Once this is done you can either delete the local copy of the project, or rename it. Then import the project in the workspace_RTC folder via the Existing Projects into Workspace option. Select the project folder and DO NOT select the option to Copy projects into workspace. That way the CE project is linked to the one in RTC.
Alongside the Project folder in workspace_RTC we usually have a second top-level folder where support files are kept and managed separately - i.e. solution deliverables. For example, property files, external scripts and stuff like externalized attribute maps. This folder also holds the 'compiled' Project Config xml. As you probably already know, every time you make a change and then Save or Run/Debug an AL in the CE, the config XML file in the Runtime-<project name> folder under your TDI workspace is updated. That's why we do NOT include the Runtime assets in the main RTC project. Otherwise all team members will constantly be (partially) updating this resource.
Instead, one person is given the task of refreshing his local project and then creating the compiled config XML file, which is then placed in the secondary folder. If this is my job, then I use the Project > Properties setting in my CE to Link to this file. That way, whenever I deliver changes, I also update the complete config XML.
After this, my day-to-day life consists of first retrieving any changes from RTC and then refreshing the project in my CE. After that I work on those items that are my responsibility and then deliver these to RTC. If others will be working on the same source files, you'll need to lock these resources until you're done with them.
Of course, if you are using one of the source management systems that can be plugged into a single Eclipse instance alongside TDI, life is a bit easier. Then you can use the Team option in the context menu for resources directly from the CE.
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