Fix Docker build script path handling for subdirectory node sources in mkconcore

[Titas-Ghosh]

Fixes #420
Hi @pradeeban ,
This PR fixes Docker script generation in mkconcore for node sources in subdirectories (for example script.py).

Problem

Generated build scripts used incorrect relative paths (../src/...) and incorrect directory return (cd ..) when Docker build directories were nested (like docker-subdir/script).
This broke Docker workflows for valid subdirectory source layouts.

Fix

• In mkconcore.py, compute Docker build directory depth and derive a correct relative prefix.
• Use that prefix for all generated cp commands to src/....
• Use matching cd <prefix> to return to the study root after each node build step.

Test

Added regression test in test_cli.py:

• test_run_command_docker_subdir_source_build_paths
• Verifies generated out/build contains correct ../../src/... copy paths and cd ../../ for subdirectory sources.

[pradeeban]

@Titas-Ghosh there are many irrelevant linechanges included in this PR in the mkconcore.py file. Perhaps an EoL character? Can you make sure your PR changes the minimal number of files and the least amount of lines necessary in the files? That will help with the PR review and maintenance of the code in the long term.

[Titas-Ghosh]

Hi @pradeeban, thanks for pointing this out, actually you have mentioned this in one of my previous PRs also , i should have been more careful , while making this PR , keeping the maintenance factor in mind . I will make sure this doesn't happen in my future PRs from now on.

I’ve cleaned the branch to keep the PR scoped to only the necessary changes only in these two files
mkconcore.py and test_cli.py