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Error at use of personal libraries in Nios II 9.1 sp1

Honored Contributor II

During transition from Nios I to Nios II, I have faced the problem: 

In Nios II 9.1 sp1, I added catalog of my libraries, after which I need to exclude some files from compilation, as libraries are the same for many projects, but different projects use different files. When I press "Exclude from build..." on file – file is flagged with another icon (disabled), but at compilation it is still in Makefile and naturally produces errors as periphery which is not used in project is described in file. Though, for files in project root (without catalogs), everything works in a correct way.  

In Nios II 11 this problem is eliminated, and everything is done in a convenient and correct way, but Quartus 11 is very buggy (SOPC-Builder as well as Qsys) and I can’t compile project normally.  

Question: either I add library catalog incorrectly (New-Folder-Advanced-Link to folder in the file system), or I need to eliminate this bug somehow in Nios II 9.1 sp1
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