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How a tool-chain integrator integrates into the MBS is documented in the CDT Plug-in Developer Guide > Programmer's Guide > Managed Build System Extensibility Document (see online here).
The Design document for the MBS in CDT 2.0, CDT 3.0 and CDT 4.0 is contained in https://bugs.eclipse.org/bugs/show_bug.cgi?id=68232. That bugzilla also contains an attachment, https://bugs.eclipse.org/bugs/attachment.cgi?id=81648, that describes the items from the design document that have not yet been implemented.
Also Multi Version toolchain support design document attached here https://bugs.eclipse.org/bugs/show_bug.cgi?id=214207.
Project Templates: CDT Plug-in Developer Guide > Programmer's Guide > Project Template Engine The following documents can be found in CDT Plug-in Developer Guide:
Useful collection of design documents is concentrated in Bug report #115935: