I have been working in Kile and I have noticed a bug as follows. 

When I have nested folders and I use the \input command, then the LaTeX 
requires that all paths be relative to the master document. However, the Kile 
scans the document using the relative path to the current file. Due to this, 
the file which I have included using the input command \input instead of coming 
under that specific file subtree from which it was \input instead appears under 
the main tree. 

For example, my structure is as follows:

/
|--------    master.tex
|--------       algebra.tex
|--------       algebra
                |--------    linear-algebra.tex
                |--------     matrices.tex

Now the input chain is as follows:

master.tex --> algebra.tex --> linear-algebra.tex --> matrices.tex

Now what kile expects is that since linear-algebra.tex and matrices.tex are in 
the same folder, matrices.tex should be included in linear-algebra.tex using 
the command 

Case A:
\input{matrices.tex}. 

However, LaTeX wants me to do this as 

Case B:
\input{algebra/matrices.tex}

When I do as in the case A, the kile project tree is proper, but LaTeX does 
not compile. In case B, LaTeX compiles but Kile project tree is screwed up. 


This bug is kind of  anti-thesis to the bug #112089[0]. I think the problem is that the relative path is relative to the parent file rather than the master document. I guess, making the relative path wrt master document should fix the things and should not be a problem to anyone


[0]: https://bugs.kde.org/show_bug.cgi?id=112089