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There is the way to store files in /Database directory (here files can survive reboot) and copy them to place where they are need to be via Post Boot script in Startup/Cron section in web-interface.
For example in my case i store udpxy binary and udpxy-startscript in /Database/udpxy/ and every boot system copy udpxy binary to /bin and run udpxystart.sh script:
cp /Database/udpxy/udpxy /bin