Is there any way to modify app permissions on a rooted (running Android 4.3) device "by hand"?
Or maybe I should ask how third party apps (like "access denied" or "Gemini") can block app permissions?
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You can use adb (Android Debug Bridge) tools.
-Install platform-tools which are included in Android SDK
-Toggle USB Debugging options on your phone.
-Connect to your phone with adb.
Example operation for testfile.txt
Upload your file with 'adb push ' command.
adb push testfile.txt /data/local/tmp/
Get shell with 'adb shell' command.
(You will get a prompt like below.)
Become superuser with 'su' command.
Change permissions of testfile.txt to 644 (-rwx--r--r-)
chmod 644 /data/local/tmp/testfile.txt