Hi,

The automatic sysroot synchronization indeed can only download the files from the root of the target filesystem. The easiest way to work around it would be to synchronize the files manually using SmarTTY, or add custom project shortcuts (requires Custom edition or higher) for downloading the arbitrary directories from arbitrary machines into the toolchain’s sysroot. Once defined as a custom shortcut,  you will be able to trigger synchronization via the Project menu.

Regarding the case sensitivity, such files will indeed override each other on the Windows side. You can try enabling the case-sensitive mode for a specific NTFS folder as described here, but this may not be handled correctly by the toolchain or Visual Studio itself. Generally, unless you are building custom kernels, this should not be a problem as this type of file name collisions is rare. If it does interfere with your projects, please consider creating an Advanced CMake-based project configured to directly access the remote filesystem via SSH. This mode will properly handle case-sensitive file names, although you would need a Linux machine to build the code.