Not sure what you are asking help for...
If you want to make it really simple, then from the top directory of your server (where the server.jar is) do this:
chmod -R 755 .
That's a dot at the end, it means the current directory and -R means recursive. 755 gives all the contents rwxr-xr-x which is fine.
Non directories dont need the x bit set, but it won't matter.
chmod is a command in Unix systems to change the mode of the file. Typically to set permissions, but there are other bits set in the mode that don't deal with permissions (to make a file sticky, or set SUID or SGID bits, which isn't relevant here)
RTFM --
type man chmod
Nonetheless, "chmod u+x file" is short hand for "add the x (execute) bit to file for the owner of the file"
Directories need to have at least r-x (5) permission to be able to read their contents.
Where are these numbers coming from? The permissions are grouped into three sets.
Permissions for "u" (the owner of the file)
Permission for "g" (the group owner of the file)
Permission for "o" (other, aka everyone else)
Each permission u, g and o is made up of three bits.
The order of the permission bits is "r", "w" and "x" for read, write and execute bits respectively.
A permission of 7 is decimal for 111 binary which means r, w and x bits are all set.
Mode 5 is decimal for 101 binary which means "r" is set, and "x" is set, but "w" is not set.
Mode of 0 is decimal for 000 binary which means no bits are set.
Mode 4 is decimal for 100 binary which means just the "r" bit is set
Mode 6 is decimal for 110 binary which means just the "r" and "w" bits are set
etc..
So if a file is modified with:
chmod 755 file
then for the owner, the permission is 7 decimal, 111 binary thus "r", "w" and "x"
for the group owner, the permission is 5 decimal, 101 binary thus "r" and "x"
for other, the permission is 5 decimal, 101 binary, thus "r" and "x"
thus if you do:
ls -l file
you'll see the permissions printed as:
rwxr-xr-x
the use of a+x or u+x or g+x etc.. is just short hand for OR'ing the bit to the existing perms.
If the file was already mode 444 (pop quiz, what does that mean?... hint read only)
Doing chmod a+x file makes the new permissions 555 (we added the "x" bit which is a 1. 4+1 = 5)
The other files in your server can simply be 644 (rw-r--r--)
The shell script "ServerStart.sh" could be set to 744 (rwxr--r--) to make it executable by the owner, but not group or other users.
If the magic is in the file (the first line is #!/bin/bash) then making the file executable means you can just type the name on the command line and if it's in your path, it'll execute.
If the file didn't have the execute bit set, you can still run it by providing it as an argument to the shell:
$ bash ServerStart.sh
With the x bit set for u (owner):
$ ServerStart.sh