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If you have the code and make system already put together, use the Import option in Eclipse rather than the New Project option.

Eclipse is dumb in it's head and can't run Linux build scripts through Cygwin. So, you have to compile with Cygwin and when you go to debug, fix the paths because Eclipse will have an image path of '/cygdrive/c/.....' for the source code that it doesn't understand. Use the command set substitute-path <cygwin-linux path> <Windows path> to fix it.

You can't use the run command with the step instruction button - it will just run to completion.

Eclipse has it's own Make auto-generation system called 'managed make': https://www.eclipse.org/org/langsymp/CDT%20Managed%20Build%20System.pdf

Note that you can set build properties (the key thing being compiler, include folders, flags, libraries, etc) on a per folder and per file basis, not just for the project top level. But it's not obvious how to force a file to accept parent settings that are different. Look at the icon of the file in the project navigator. If you see a little blue wrench, it means it has a build configuration that is different from the parent. You can click and select to restore defaults to put it back where it needs to go.

More on Cygwin

If you run into this problem when compiling fatal error: can't open /tmp/ccc6IHTT.s for writing it probably means you have another cygwin1.dll in your path (check C:\Windows, which seems to get included despite not being explicitly in the path).

Workspaces

To remove one: use the menu Window > Preferences, then go to General > Startup and Shutdown > Workspaces.

Can you enable deletion of a workspace folder if you remove the .lock file from the .metadata folder?

Deciphering Errors

If you get a "cannot find -l<libraryname>" error, then this probably means that there's a .so that it can't locate or is not being built.

If the app won't launch with a certain workspace and you see a null pointer exception error in the launch terminal, you may need to kill the workbench.xmi file. Deleting <workspace>/.metadata/.plugins/org.eclipse.e4.workbench/workbench.xmi solved the problem.

Options

To stop it from re-building on Debug launch, Preferences -> Run/Debug -> Launching, and uncheck "Build (if required) before launching"