Properly indent -json CLI output for readability

[jahedullah]

Description:
Fixes the JSON format for -json CLI output by adding proper indentation, making it much more readable.

Testing:
Built a local Docker image and ran it against two commits; the output formatting was correct in both cases with proper indentation. The generated JSON file looks much better now.

[tsantalis]

@jahedullah
Thank you for your contribution in RefactoringMiner.
We have some tests the depend on the JSON output.
For example, /RefactoringMiner/src/test/java/org/refactoringminer/test/TestCommandLine.java
This test is not running in the CI, because it takes time, but I am running it locally. I am sure it would fail.

Moreover, our Chrome extension depends on the JSON, and I would need first to test that the new formatting does not break anything there.

In my opinion, the risks (i.e., breaking tests, breaking dependent projects) from this PR outweigh the benefits (i.e., JSON formatting).