Ok, here is what I did.
As it was suggested by @Raphink, I used tocloft
package. All of the sections that I wanted to be at the top level of my TOC (such as contributions, summary, references, etc) I included in TOC as parts. This is because I haven't found a way to adjust only certain sections without changing all sections in TOC. I also don't have any parts in my report, so it doesn't conflict with any existing items.
Then, in order to format them correctly (as regular sections, but with no indentation) I used the following:
\renewcommand{\cftpartfont}{\normalfont} % make parts look like sections in TOC
\renewcommand{\cftpartpagefont}{\normalfont}
\setlength{\cftbeforepartskip}{0pt} % remove spaces before and after chapters
It looks a little clumsy, so if someone knows a better solution, please post your reply.
As for LoF and LoT, I used the following:
\setlength{\cftfigindent}{0pt} % remove indentation from figures in lof
\setlength{\cfttabindent}{0pt} % remove indentation from tables in lot
Hope someone else finds it helpful!
From the linked question in the comments, I figured out the following:
\makeatletter
\renewcommand*\l@figure{\@dottedtocline{1}{1em}{3.2em}}
\makeatother
Which produces:

Best Answer
You may want to say something like
or even
1em
: experiment with the added width. The code should go in the preamble.The relevant section in the manual is 9.2.2