Update `run` script to honor `$JAVA_HOME`, if set

What are the goals of this MR?

• Update run script to honor $JAVA_HOME, if set.

Are there any tricky things testers should keep an eye out for?

• No

• Yes, as follows:

• I have tested these changes thoroughly.

• This requires extra testing due to changes to architecture or other similarly risky changes.

• I used the Thanos Tool for any JSON edits, I did not edit any JSON files by hand (MR will be rejected if there are manual JSON edits).

• I acknowledge that this contribution will be released under the AGPL license.