Standardize Port Usage: Replace Port 3000 with 8888#7
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This PR updates all occurrences of port 3000 to port 8888 to align with the default port used by UnityMol and GROMACS for IMD (Interactive Molecular Dynamics) communication.
Dependency:
⚠️ This PR depends on another PR Hotfix/build workflow fix: #8
Please ensure that the linked PR is merged (and tested) before merging this one to avoid breaking compatibility.