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Answer to question 1: Can you post a minimum working example?  latexdiff will not track changes in the preamble (with a few pre-defined exceptions), but should track yext between \begin{abstract} and \end{abstract}.  If your format really uses \abstract{text} look up the --append-textcmd option of latexdiff.

Note: Edited in response to the next answer to fix a wrongly-remembered option name

Thank you very much Frederik. 

I have tried -append-textcmd="abstract", but still not work.

Following  you suggestion of using add-textcmd given this error "Unknown option: add-textcmd".  I upload a MWE here. The .cls was not allowed to upload, so I zipped it.

Any help would be appreciated.

The problem is that the \abstract command is given in the preamble, which is not parsed in the same way. So you need to do this instead:

latexdiff --append-context2cmd="abstract" old.tex new.tex > diff.tex

The diff.tex files looks what I would expect, although I did not test whether it compiles (if it doesn't then there is likely some incompatibility between mdpi.cls and ulem.sty, which I cannot really help you with - you would need to use a different markup style in that case (option -t)

PS: I gave you the wrong option name in my previous answer but you figured out the correct one - I have fixed it above in order not to confuse future readers

Hi, Frederik

Thank you again for the answer. You were right. The --type UNDERLINE not work but CTRADITIONAL TRADITIONAL CFONT FONTSTRIKE INVISIBLE  can be used to compile PDF as following code:

"latexdiff --t CTRADITIONAL --append-context2cmd="abstract" old.tex new.tex > diff.tex".

The problem is solved.

I use LyX as a front end for LaTeX for this very reason. LyX has an excellent change tracking feature. 

Probably you need github: https://github.com/

github is specially designed to track changes in codes (all programming codes: be it R, LaTeX, python, etc): It enables you to check up versions and control changes in your previous and past works by highlighting the added lines (green) and deleted lines (red) in your LaTeX code text. You need to sign up first for the github, then upload your code and share the link with your supervisor. You both will then see your weekly progress. By the way, I have a presentation exactly on this topic: how to check up updates in research papers for both parties (student-supervisor):

Deleted research item The research item mentioned here has been deleted

in github you need to submit following code:

1. git diff (it will check up the changes in your text versions)

2. git commit -a -m (it will commit changes in your work)

3. git push (it will upload the new version in to the git environment).

Alternatively (perhaps, more user-friendly), you can simply drag and drop your files into your repository.

For each project you need to create separate repository. For example, you can have a look at mine: https://github.com/paulinelemenkova