I have experienced an issue with using a local repository with sync. I checked out the source to see if that would clear up what may be causing this issue, but I'm still not clear what is causing this issue.
org-sync with several .org filesorg-sync as a local directory sync.org files as expectedLast synced notebook and latest remote notebook differcontent://com.android.providers.downloads.documents/tree/msd%3A73372.org files were created outsize of orgzly, but are valid .org files (and very simple).org file created in orgzlyBackground: "Remote" is the files that aren't Orgzly's internal copy of the notebooks. Somewhat confusingly, that means when your repository is local, the local files on the phone (but outside Orgzly) are referred to as "remote". (This makes more sense when they really are remote, as in the other repository types, which sync with something outside the phone.) This may or may not be at issue here, just throwing it out there in case it helps.
The error message: just means that you've editted one of the notebooks both within Orgzly and outside Orgzly since you last synced, or at least _that Orgzly believes so._ There could be cases where no edits are made but something updates the timestamp on the file/notebook; or there could conceivably be a bug (whether in Orgzly or in the phone) where timestamps are seen incorrectly somehow.
If you know you didn't edit the files outside Orgzly, it may be worth double-checking the modified time on the files in the local folder. If that doesn't reveal that they were updated somehow, I think there are settings in Orgzly to display more of the various timestamps on the notebook list screen. Wouldn't necessarily show what's updating the files (if it is that), but would help confirm or deny _whether_ something is updating them.
One condition that I found while troubleshooting further is orgzly was not throwing an error, but in the sync directory it was creating a new file on each orgzly sync like below (with ls -l). I'm curious under what condition this might happen and if this lends a hint at what's going on?
-rw-rw---- 1 root everybody 48197 Apr 3 07:20 personal.org
-rw-rw---- 1 root everybody 48197 Apr 3 07:22 'personal.org (1)'
-rw-rw---- 1 root everybody 48207 Apr 3 07:23 'personal.org (2)'
-rw-rw---- 1 root everybody 48207 Apr 3 07:23 'personal.org (3)'
-rw-rw---- 1 root everybody 48118 Apr 3 07:24 'personal.org (4)'
-rw-rw---- 1 root everybody 48124 Apr 3 07:25 'personal.org (5)'
-rw-rw---- 1 root everybody 48124 Apr 3 07:27 'personal.org (6)'
Ok, I believe I found the problem 馃帀! I will leave some notes below to hopefully help other folks who run into this in the future. Thanks for taking a look @ScottFreeCode!
tl:dr: This was caused by a quirk relating to termux internal and external storage.
To use orgzly (or any other app) correctly with folders/files that you are interacting with using termux, you must access these folders/files using ~/shared/* in termux. An example would be to access a folder in the Downloads folder by this path ~/shared/Download/org-sync from termux as opposed to ~/downloads/org-sync.
Alternatively, when you are selecting a directory in orgzly to sync with, from the Android Files app, you can select Open With => Termux, then select the directory you would like to sync.
And yes, this seems to work, even using git within termux for version control 馃帀.
Please let me know if you have any questions, I an happy to help.