[2201.6.x] Improve bal tool with changes to class loading and packing jars from directory paths

[gayaldassanayake]

Purpose

$subject

U6 PR of #40567
Fixes #40264

Approach

Describe how you are implementing the solutions along with the design details.

Samples

Provide high-level details about the samples related to this feature.

Remarks

List any other known issues, related PRs, TODO items, or any other notes related to the PR.

Check List

• Read the Contributing Guide
• Updated Change Log
• Checked Tooling Support (#)
• Added necessary tests
  • Unit Tests
  • Spec Conformance Tests
  • Integration Tests
  • Ballerina By Example Tests
• Increased Test Coverage
• Added necessary documentation
  • API documentation
  • Module documentation in Module.md files
  • Ballerina By Examples

[gayaldassanayake]

Closing the PR since the changes are already added to 6.x