High level overview:

• This only concerns mtime (and its equivalents on other systems, if applicable). atime, ctime and permissions are out of scope.
• An object added to an annex and later retrieved from it via mv, cp -L, git annex unannex and such should always keep its mtime, even if retrieved on an entirely different machine and/or from a backend that doesn't support timestamps natively.
• If an added/reinjected object is already known to the annex, use the older mtime by default, since that's probably the version that's had its metadata preserved better.
  • If that's too much of an assumption, provide a switch to use the older/newer/known/unknown mtime, or add a git-annex-touch command.
• symlink and object file mtimes should reflect the mtime tracked by the annex.
• ideally, directory mtimes would also be preserved, or failing that, git-annex-fix, git-annex-add and git-checkout should leave them untouched.

open questions/ideas:

• What if the user touches a file/symlink, bypassing git-annex? Should the data be reconciled or ignored?
• preserving directory mtimes looks tricky, but could it maybe be done from a hook or two?

notabug --Joey