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If an autoconf project is not shared (i.e. if "Secure Copy" or "Smart Secure Copy" is selected for the remote server), then such project can not be built on remote host. The reason is that in copying sync modes, IDE considers all makefiles reside on local host, so it copies them to the remote host. So autogenerated makefiles on remote host are overwritten by local ones and build fails.
Please evaluate
The statement isn't correct. Such projects now can be build. The rest of the issue is described in issue 174881 (Smart secure copy: don't override generated files with local changes)