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Update 20190226: As detailed in the Restic issue linked below, this seems to have stopped working. The original binaries I created with this method continue to work without errors for some strange reason, but I can't give access to new binaries directly using this method.

After some preliminary testing, it looks like a slightly less hacky workaround is to compile a binary (using a compiled language) that calls your bash script. Add that binary to FDA and it seems to work. Add to the root-owned /Library/LaunchDaemons plist, and you have a way to call it from root without all the craziness above`.

For security, I sudo chown root and sudo chmod 0700 the resulting binary before adding to Full Disk Access (although admittedly an attacker could just change the bash script that this calls if it were left undetected).

After some preliminary testing, it looks like a slightly less hacky workaround is to compile a binary (using a compiled language) that calls your bash script. Add that binary to FDA and it seems to work. Add to the root-owned /Library/LaunchDaemons plist, and you have a way to call it from root without all the craziness above.

For security, I sudo chown root and sudo chmod 0700 the resulting binary before adding to Full Disk Access (although admittedly an attacker could just change the bash script that this calls if it were left unprotected).

My solution is a totally hacky workaround, but doesn't require whitelisting bash entirely.

My solution is a totally hacky workaround, but doesn't require whitelisting bash entirely. Update: Slightly less hacky workaround below.

UPDATE:

After some preliminary testing, it looks like a slightly less hacky workaround is to compile a binary (using a compiled language) that calls your bash script. Add that binary to FDA and it seems to work. Add to the root-owned /Library/LaunchDaemons plist, and you have a way to call it from root without all the craziness above`.

Example script in Go:

// Runrestic provides a binary to run my restic backup script in MacOS Mojave with Full Disk Access
package main

import (
    "log"
    "os"
    "os/exec"
    "path/filepath"
)

func main() {
    ex, err := os.Executable()
    if err != nil {
        log.Fatal(err)
    }
    dir := filepath.Dir(ex)
    script := filepath.Join(dir, "restic-backup.sh")
    cmd := exec.Command("/usr/local/bin/bash", script)
    if err := cmd.Run(); err != nil {
        log.Fatal(err)
    }
}

For security, I sudo chown root and sudo chmod 0700 the resulting binary before adding to Full Disk Access (although admittedly an attacker could just change the bash script that this calls if it were left undetected).