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I start using eclipse CDT. As I was trying to create project in C. I have to encounter with these options. When I select makefile project. I had options to choose toolchain from these GNU AutoChain, Linux GCC, Cross GCC. What will be difference if any one of these toolchain I select.

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GNU Autotoolchain:

autotoochain ,generally i would say use autotools if you have a big Project to distribute.

Linux GCC

is just a compiler system for compiling and distributing your product. You can not do cross compiling with normal gcc, also you have to provide your own Makefile to compile (if you need one).

Cross-Compiling (Cross GCC)

Also a GCC-Compiler but made for cross-compiling. For example you can write and compile an applicaiotn on your own x64 or x86-Bit PC for running on for example ARM-Platforms. Wiki Cross-Compiler

Search also for CMAKE.

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