footnotes - on the bottom except on last page of chapter

No automated solution, but perhaps \enlargethispage can help. It should quite easy to measure the gap between text and footnotes on the last chapter page and issue an \enlargethispage{-??\baselineskip}, where ?? stands for the number of lines to cut from the page.

Let's hope that the among the requirements there's a page number at the bottom.

Of course this should be done when the text is completely definitive.

I don't know if there's an automatic way to do this, and the following solution obviously can't be made part of your class file, but if you want to add some instructions on how to achieve it manually once you have finished the whole thesis, you can do the following. For the last page of a chapter, you need to set the footnotes in a minipage. You do this by putting \footnotemark in the place in the text where you need the footnote (instead of the regular \footnote command) and then putting the \footnotetext commands inside the minipage. If you have multiple footnotes on the page, you need to manually step the mpfootnote counter for each subsequent \footnotetext command. Perhaps others have a more automated solution.

\documentclass{report}
\usepackage{calc}
\usepackage{lipsum}

\begin{document}

\chapter{A chapter}
\lipsum*[1]\footnote{A regular footnote}\par
\lipsum[2-4]\lipsum*[5]\ A footnote here.\footnotemark\par
\lipsum[6]\ Another footnote here\footnotemark\par
\lipsum[7]

\noindent
\begin{minipage}{\textwidth}
  \setcounter{mpfootnote}{\value{footnote}-1}%
  \renewcommand{\thempfootnote}{\arabic{mpfootnote}}
  \footnotetext{The second last footnote.}
  \stepcounter{mpfootnote}
  \footnotetext{The last footnote.}
\end{minipage}
\end{document}