Q:

Where should index and glossary appear in a report? 

I am writing my thesis and now wonder whether I should typeset index and glossary as an appendix or after them. 
There's no department-level accepted writing style, so my adviser's opinion might be different from that of my thesis committee.  Hence, I am not only supposed to be accountable for my scientific participation; but also the typesetting and formatting of the thesis.  This is why I am looking for a justifiable answer.  For better or worse, the common practice for scientific writing style in Farsi (which I am supposed to present my thesis in) is to adopt and adapt style guides of English.  

A:

The answer is for you to do what the universoty or your department requires.  There is no universal answer to this.  
For academic writing in English, one would likely be using the APA Style Guide or the MLA Style Guide. ( See this question for more on style guides in general.)  Different departments may have different standards, so check with your advisor.  
There may be a university style guide for you to follow, to handle issues specific to your educational institution.  There may even be more than one, so make sure you're using the right guide. ( Here's an example of a thesis style guide, but this will almost certainly not apply to your school.) 
The bottom line: Check what style guides your university requires and use those. 