Re: is this data corruption?

> On December 30, 2022 7:18 PM, Samuel Wales wrote:
>>i am not subscribed, but am of the impression that's ok.  please copy me
>> directly.
>>
>>
>>tldr: git diff is showing differences that do not exist in the files
>> themselves.
>>
>>i have nothing staged, nothing fancy like stashing, etc.  this is a repo of
>> mostly
>>emacs org mode files.  mostly ascii text.
>>
>>git status and these commands show nothing unusual:
>>
>>    git fsck --strict --no-dangling
>>    git gc --prune="0 days"
>>
>>
>>the problem that seems like data corruption is that a few lines appear
>> twice as -
>>and once as +.  but in the current version of the files, those lines exist
>> only once.
>>here are the lines.  there are 2 - versions and one + version:
>>
>>+***************** REF bigpart is a partition biglike and homelike are
>>+distracting nonsense i think except to describe inferior filesets.
>>+anomalous subset of home might be called homelike or so.
>>
>>
>>emacs magit shows the same problem.  however, it shows a slightly different
>> diff.
>>i did a meta-diff on git diff vs. magit, and there are about 800 +
>> real-content lines
>>that magit shows but git diff does not.  i do not know what this means.  wc
>> -l is like
>>
>>  62540 aaa.diff
>>  62965 bbb--magit.txt
>>
>>idk why a diff would be different with only + lines being different?
>>
>>
>>in summary, what is wrong with my repo, if anything, and what can i do
>> about it?
>>nothing on the web for git corruption seems to say much, other than pull
>> from
>>github or whatever.  this is my own repo, the original repo, so i cannot do
>> that.  org
>>annex has an uncorrupt tool of some kind, but it did not seem relevant.  i
>> do have
>>rsnapshot [basically rsync] backups of the repo and the most significant
>> files and
>>dirs, but i do not know what one does to use that to repair any issues.  i
>> won't get
>>into why, but changes were made over months.
>>
>>is there a protocol for this?
>>
>>would git fsck have balked?
>>
>>thank you!
>>
>>
>>p.s.
>>
>>i have no reason to believe this is related, but git diff has intermingled
>> emacs org
>>mode entries.  but i don't have to talk about it in org terms; in generic
>> text terms, it
>>has intermingled parts of different paragraphs.  as a user, i'd prefer
>> that
>>completely unrelated paragraphs not be mingled, regardless of minimality.
>> if
>>possible.
>>
>>with respect to the intermingling only, unless this is related to the
>> possible
>>corruption, i will presume the diff is correct, in that a patch from it
>> would produce
>>the same result as a patch that does not intermingle.  i believe this
>> intermingling is
>>because diff does not understand org, or paragraphs for that matter.  in
>> org, an
>>entry starts with "^[*]+ " and ends at the beginning of another entry or at
>> eof.
>>they consist in my case mostly of ascii text paragraphs.  just as with
>> paragraphs, if
>>you move an entry, you don't expect it to be mingled with a different one
>> in the
>>diff.
>>
>>i have been told that this cannot be fixed by merely telling a slightly
>> improved
>>differ that stuff between stars is worth preserving, but that a parser, not
>> merely a
>>couple of regexps, is needed to reduce this intermingling.  i have also
>> been told
>>that difftastic uses tree-sitter, which might get such a syntax for emacs
>> org mode.
>>and so maybe at some point git diff can use that.  idk.
>>
>>idk if any of this is related but i include it for completeness.
>>
>>also, please don't laugh, but i am using git version 2.11.0.  i will
>> upgrade pending
>>various library and os stuff but my main concern is not for git, but for
>> possible
>>corruption in the repo and what is possible to do, at least given
>> rsnapshot, to fix it.
>
> I cannot account for your emacs issues, but have a question. Have you done
> any git add operations? Git diff is subject to what specifically is staged.
> So you might be comparing your file with partially staged content that could
> account for partial diffs. See if diff --cached makes a difference. Also try
> different algorithms, like --patience or --diff-algorithm=histogram.
>
> --Randall
>
>