What changes should be notated in a journal resubmission? I am currently in the process of submitting a manuscript to a journal.  During this process my manuscript has come back for revision, and the journal has asked for an updated manuscript with revisions annotated.  What level of changes should be annotated?  Similarly is it acceptable to provide a generic comment when changes are for flow and not for content (e.g. "sentence rephrased for clarity")?

As an example (in my perceived order of required-ness):


Adding or removing significant content (figures, paragraphs, sentences)
Rephrasing a sentence changing the meaning
Rephrasing a sentence changing the grammar, but not the meaning
Adding/removing words that are superfluous (or change the meaning in an insignificant way)
alteration of comma's, periods, etc.
An editor once "requested" that I submit a "tracked changes" or latexdiff version of my resubmission if I wanted him to deal with it in a timely fashion. Since then, my strategy has been to submit:


revised manuscript (no annotation);
latexdiff of revisions against version submitted last time, to highlight every last comma changed;
cover letter, describing all scientific changes plus any major textual changes ("we substantially rewrote the methods section in an attempt to improve its clarity"). I refer the editor to the diff for minor textual corrections.


No editor has complained yet... ;)