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Stop Java from killing Bash script that started it

I've spent the past couple days working on this, and at this point I am super stuck. I have a Java program that must be run not as a service. This program must also be capable of updating itself when a new file is given for updating.
As a result, I have a script that is started with Linux that starts the Java application and then checks every 5 seconds if the application has been terminated. If the application has been terminated, it should check if there is an update and then start appropriately.
This is the code for that script:
#!/bin/bash
JAVA_HOME=/usr/lib/jvm/java-16-openjdk-amd64
WORKING_DIR=~/Data
LOG=$WORKING_DIR/logs/Bash.log
rm $LOG
echo "Script started" > $LOG
while true; do
source $WORKING_DIR/Server.pid
if ! kill -0 $AppPID; then
echo "App must be started" >> $LOG
source $WORKING_DIR/UpdateStatus
if [ "$UpdateReady" -eq "1" ]; then
echo "Moving files for update" >> $LOG
mv $WORKING_DIR/Server.jar $WORKING_DIR/old.jar
mv $WORKING_DIR/new.jar $WORKING_DIR/Server.jar
fi
nohup ${JAVA_HOME}/bin/java -jar ${WORKING_DIR}/Server.jar &
echo AppPID="$!" > $WORKING_DIR/Server.pid
echo "Server started" >> $LOG
if [ "$UpdateReady" -eq "1" ]; then
echo "Checking for safe update" >> $LOG
source $WORKING_DIR/Server.pid
echo UpdateReady="0" > $WORKING_DIR/UpdateStatus
sleep 5;
if kill -0 $AppPID; then
echo "Update successful" >> $LOG
rm $WORKING_DIR/old.jar
else
echo "Update failed, restarting old jar" >> $LOG
rm $WORKING_DIR/Server.jar
mv $WORKING_DIR/old.jar $WORKING_DIR/Server.jar
nohup ${JAVA_HOME}/bin/java -jar ${WORKING_DIR}/Server.jar &
echo AppPID="$!" > $WORKING_DIR/Server.pid
fi
fi
echo "Server start process finished, going into idle state" >> $LOG
fi
sleep 5
echo "5 seconds idle passed" >> $LOG
done
To initialize the update, I have tried a couple of different things, both with the same result. First I had set UpdateReady="1" through Java, then used exit(0);. I have also tried having Java call a Bash script which also sets UpdateReady="1" but uses kill $AppPID to shutdown the java application.
The result is that both the Java application and the Bash script stop executing causing the update and restart to fail! I have looked through a significant amount of Stack Overflow questions and answers finding things such as nohup, all to no avail.
I will once again state that the Java application cannot be run as a service. No packages other than what is included in Java or made by Apache can be used, and no programs can be installed to Linux. I would prefer to solve the problem with Bash.
Upon testing some things mentioned in comments, I may have missed something that turns out to be important. While all other runs of the startup script will be run by the startup applications manager, the initial run is not.
The install is taken care of remotely with an SSH connection sending the following command string:
cd /home/UserName; unzip -u -o Server.zip; chmod 777 install.sh; bash install.sh &; exit
install.sh is as follows:
#!/bin/bash
INSTALL_DIR=~/Data
mkdir ${INSTALL_DIR}
mkdir ${INSTALL_DIR}/logs
mkdir ${INSTALL_DIR}/data
cp Server.jar ${INSTALL_DIR}/Server.jar
cp service-start.sh ${INSTALL_DIR}/service-start.sh
chmod 777 ${INSTALL_DIR}/service-start.sh
rm Server.jar
rm service-start.sh
rm Server.zip
nohup bash $INSTALL_DIR/service-start.sh &
Upon rebooting my machine, I noticed that this problem goes away! This means that there must be a problem with the initial setup script. When the shell command is run, it does seem to be sticky and not actually let go after the bash install.sh &. I have tried putting nohup at the beginning of this, however the entire line will not run in that case for reasons I am not able to determine.
I would prefer to not have the user be forced to restart after install and can't seem to find any way to force the Startup Application manager to start an application at any time other than startup.

Well, after a lot of searching and some prompting from the comments, I found that the issue lied with how the program was initially being started.
As mentioned in the update, the first run is always started by an ssh connection. I knew there was a slight problem with this ssh connection, as it seemed to hold onto the connection no matter what I did. It turns out that this was causing the problem that resulted in the Bash instance and the Java instance remaining attached.
The solution for this problem was found here: jsch ChannelExec run a .sh script with nohup "lose" some commands
After managing to get the initial setup to start with nohup properly, the issue has gone away.

Git Hook PHP Script: No Output

I have this Script php-pull-script.phpwritten:
<?php
$output1 = shell_exec('git pull');
$output2 = shell_exec('pkill java');
$output3 = shell_exec('mvn package');
$output4 = shell_exec('java -jar ./target/compute-0.0.1-SNAPSHOT.jar');
echo "<pre>$output1</pre>";
echo "<pre>$output2</pre>";
echo "<pre>$output3</pre>";
echo "<pre>$output4</pre>";
?>
When executing in shell, I am not seeing any output in order to verify that it is running. I am not sure at all it is working. Is there a better way to do this automation script?

How to send of the java command with shell_exec and leave it running in background (Is & possible with shell exec)?
test.php
<?php
shell_exec('test.sh');
test.sh
echo "Do something"
/bin/sh -c 'sleep 10' >> /dev/null 2>&1 &
exit 0
/dev/null can be also a path to an logfile
All pathes here and in phpscript should be absolute, like: /path/tomy/test.sh
Here the test.php doesnt wait 10 seconds for the subcall.
Hope that helps a little ;)

You might not be in the correct working directory. You may need to set that manually to make the commands run. Otherwise, those commands look right. Though you really should just have this set up as a shell script. PHP's not a good language for this sort of thing, and if you are calling this from a REST endpoint there are far better solutions like Jenkins.

HOME environment variable not set in bash script

I have a Java program that spawns a bash script that calls another script. In that second script, I'm finding that the $HOME variable is not set. Here's the gist of it:
In Java:
Process p = new ProcessBuilder("bash", "-l", "/foo/a.sh").start();
// code to actually execute p
/foo/a.sh:
#!/bin/bash
/foo/b.sh
/foo/b.sh:
#!/bin/bash
echo "HOME=$HOME"
This echoes "HOME=". The eventual problem is that $HOME/bin is supposed to be added to my PATH in ~/.profile, but since that's not happening, a bunch of custom executables aren't being made accessible.
I worked around it by doing:
if [ -d ~/bin ] ; then
PATH=~/bin:"$PATH"
fi
And that works fine. But I guess I just want to understand why $HOME wasn't being set. It seems like $HOME and ~ should be largely equivalent, no? There's probably something I'm fundamentally missing about how this environment is getting set up.
I am running Ubuntu 12.04.5, if that makes a difference.

The evidence suggests that HOME is missing from the environment in which the Java app is running. Assuming that the app doesn't explicit unset HOME, the most likely reason is that the app is being started from some context other than a login by the user the app is running as.
It's correct that ~ and $HOME are similar. If HOME is present in the environment, even if it is set to the empty string, ~ will be replaced with $HOME. However, if HOME is not present in the environment, bash will attempt to find the home directory for the currently logged in user, and use that for ~.
eg.
$ bash -c 'echo ~'
/home/rici
$ HOME='Hello, world!' bash -c 'echo ~'
Hello, world!
$ HOME= bash -c 'echo ~'
$ (unset HOME; bash -c 'echo ~';)
/home/rici
Since your workaround requires the equivalent of the last scenario, I conclude that HOME has not been set, or has been unset.

How to create a script to restart a JAR file and get output in a terminal?

I have used the following scripting for start and stop a jar file.
**start.sh**
#!/bin/bash
nohup nice java -jar Server.jar > ./Server.out 2>&1 &
**stop.sh**
#!/bin/bash
kill `ps -ef | grep Server.jar | grep -v grep | awk '{ print $2 }'`
Now I want to merge both scripts and create a new restart script. I also want this script output in a terminal instead of a text file(Server.out).
Would appreciate any kind of input/help.

You can either put the commands of the two sripts after each other (kill first, java second) or just call the two scipts in the appropriate order.
The idea is that restart is basically equivalent to killing the current running version and starting a new one.
To avoid the output to a file, remove the > ./Server.out part.
Edit: removed note about removing the redirection part as I misread the grep part of the kill script
Update: Missed the nohup part of the script: with nohup you need to redirect output to a file, because the process is detached from the terminal (see documentation). If you do want to see the output in the terminal, remove nohup as well as the redirection to the file

start-stop-daemon and java program

I'm having a heck of a time getting a java program to launch properly in an init script using start-stop-daemon. I've written the init script and it seems to run but there's never a process afterward representing the running program.
Here's a snippet of my init script
#! /bin/sh
#
#
DAEMON="/usr/bin/java"
DAEMON_ARGS="-server -cp <bunch of RMI arguments and classpath stuff> -jar <absolute path>/myprog.jar"
PIDFILE="/var/run/myprog.pid"
case "$1" in
start)
echo -n "Starting myprog"
start-stop-daemon --start --pidfile "$PIDFILE" --chuid "myuser" --verbose --background --make-pidfile --startas "$DAEMON" -- $DAEMON_ARGS
echo "."
;;
When I try to launch it via /etc/init.d I get the following:
/etc/init.d# /etc/init.d/myscript start
Starting myprogStarting /usr/bin/java...
Detatching to start /usr/bin/java...done.
.
Afterward, there is no java interpreter process running, executing myprog.jar
I've tried various combinations of --exec, --start with more or less the same results. If I could get some more visibility into what is going on, I'm sure I could figure this out but I'm not sure how to do even that.
Any suggestions?
(I'm running Angstrom on an embedded ARM platform so Java Service Wrapper isn't really an viable option, ie. I don't think its available for ARM)
I'm stuck so any advice would be really appreciated.
Thanks.

Two things to try, first try removing --startas and use --exec instead like so:
start-stop-daemon --start --pidfile "$PIDFILE" --chuid "myuser" --verbose --background --make-pidfile --exec "$DAEMON" -- $DAEMON_ARGS
Second since you are using --background try specifying the --chdir option, if you don't the working directory ends up being /.
I ended up stumbling on your question trying to solve my issue which eventually was resolved by --chdir, I believe it will resolve yours as well.

you're looking for a way to run and be able to monitor it?
have you tried ms batch dos programming it yet?
for example
#echo off
cd DirectoryOfFiles
echo "Starting up..."
java -Xmx512m mainFile
pause
mainFile = main.java?
DirectoryOfFiles = the directory you have all the class files in, if running file is same directory just remove this line
hopefully this is what you're asking for