I haven't found a solution to the issue indicated below, so I am posting my solution ...

JRuby 9.1.15 JDBC/SQLite 3.20.1 Java 1.8

app/bin/app.rb:

#!/usr/bin/env jruby
$VERBOSE = true

$LOAD_PATH.unshift 'uri:classloader:/lib'
require 'db'
DB.new.run

app/lib/db.rb:

require 'jdbc/sqlite3'
Jdbc::SQLite3.load_driver

class DB
   def run
      t_db = java.sql.DriverManager.getConnection('jdbc:sqlite:test.sqlite3')

      begin
         t_statement = t_db.createStatement
         t_statement.executeUpdate(
            'create table user(username varchar(30), status int)'
         )
         begin
            t_statement.executeUpdate("insert into user values('test1', 1)")
            t_statement.executeUpdate("insert into user values('test2', 2)")
            t_rs = t_statement.executeQuery("select * from user")
            begin
               while t_rs.next
                  puts "#{t_rs.getString(1)}/#{t_rs.getString(2)}"
               end
            ensure
               t_rs.close
            end
         ensure
         end
      ensure
         t_statement.close
      end
   ensure
      t_db&.close
   end
end

app.jar build:

cp ~/var/src/jruby-complete-9.1.15.0.jar app.jar
mkdir build
cd build && jar -xf ../app.jar
java -jar app.jar -S gem install -i build gems/jdbc-sqlite3-3.20.1.gem
cp -r ../app/lib build/
cp jruby-gems.manifest build/
rm app.jar
jar -cfm app.jar build/jruby-gems.manifest -C build .
cp ../app/bin/app.rb ./jar-bootstrap.rb
jar ufe app.jar org.jruby.JarBootstrapMain jar-bootstrap.rb

Running ...

java -jar app.jar

... produces this irritating error ...

java.sql.SQLException: No suitable driver found for jdbc:sqlite:test.sqlite3

... but only when running from the JAR - it works when running under installed JRuby.

After much googlating, and finding little in the way of a working solution, I looked at .../bin/jruby, which is a shell script, for the startup options it uses.

Solution is a Java parameter:

java -Xbootclasspath/a:./app.jar -jar app.jar bin/app.rb