What I will probably do is have the upgrader check for the presence of a .htaccess file in root. If it exists, an extra step will be added on the UI instructing the user to compare/diff their .htaccess file with recommended.htaccess for any changes that need merging. Or, I may have file integrity scan check for it.

Automated response: Inform of potential .htaccess changes

This patch adds an extra step on the upgrader after file integrity scan if .htaccess exists. It informs the user to compare / diff with recommended.htaccess and merge in any relevant changes.

A hotfix (a TAR of files to upload) has been uploaded to this issue. Only apply this hotfix if you absolutely need it and cannot wait until the next release of Composr (releases are more reliable and strictly tested). As of Composr version 11, the recommended way to apply a hotfix is by following the same steps as an upgrade (https://baseurl/upgrader.php, use the hotfix on the step “Transfer across new/updated files”). The upgrader will automatically skip files belonging to addons you do not have installed or that are newer on disk than in the hotfix. Otherwise, you can manually extract and replace these files (do not replace if your on-disk file is newer than the one in the hotfix). Always take backups of your site or at least files you are replacing before applying a hotfix. Not sure how to extract TAR files to your Windows computer? Try 7-zip (http://www.7-zip.org/).

Note: This issue was originally reported for v10. But v10 is only accepting critical bug fixes, so the patch / fix above is for v11. A fix will not be made for v10.