feat: [REQ-008] Add CockpitServer on port 6051

[sonthien22501]

Summary

This PR implements the backend infrastructure for the "Researcher Cockpit" browser extension, satisfying REQ-008 (Bidirectional Communication).

It introduces a lightweight HTTP server (CockpitServer) running inside JabRef that allows external browser plugins to communicate with the active JabRef instance.

Technical Details

• New Class: org.jabref.gui.remote.CockpitServer
• Port: 6051 (Chosen to avoid conflict with JabRef's existing internal remote port 6050).
• Endpoints Implemented:
  • GET /ping: Returns connectivity status.
  • POST /check-existence: Accepts a JSON payload ({"url": "..."}) and currently returns a mocked response.
• Concurrency: The server runs on a separate thread to avoid blocking the JavaFX UI.

How to Test

1. Run JabRef from IntelliJ.
2. Verify console log: Researcher Cockpit Server started on port 6051.
3. Open a terminal or browser and access http://localhost:6051/ping.
4. Expected response: {"status": "connected", "message": "JabRef is listening!"}.

Checklist

• Server starts/stops with JabRef.
• CORS headers enabled (allows browser extension access).
• No conflict with existing remote listener.

Closes _____

Steps to test

Mandatory checks

• I own the copyright of the code submitted and I license it under the MIT license
• [.] I manually tested my changes in running JabRef (always required)
• [.] I added JUnit tests for changes (if applicable)
• [.] I added screenshots in the PR description (if change is visible to the user)
• [.] I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
• [.] I checked the user documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

[github-actions]

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[koppor]

Code should go into jabsrv

[koppor]

Code should go into jabsrv

I mean: integrated there. Read the code there. Especially resources and GSon.

[sonthien22501]

Changes in this update:

• Moved Logic: Extracted the business logic out of CockpitServer into a dedicated resource: org.jabref.http.server.resources.CheckExistenceResource.

• Implemented DTOs: Created CheckExistenceRequest and CheckExistenceResponse in org.jabref.http.dto to strictly define the JSON structure.

• Adopted Gson: Replaced all manual string concatenation with Gson serialization for safety and consistency.

• Package Structure: Ensured all files are correctly placed in the jabsrv module.

[jabref-machine]

Your code currently does not meet JabRef's code guidelines. IntelliJ auto format covers some cases. There seem to be issues with your code style and autoformat configuration. Please reformat your code (Ctrl+Alt+L) and commit, then push.

In special cases, consider using // formatter:off and // formatter:on annotations to allow deviation from the code style.

[koppor]

Seems that the AI is not configured properly. Please guide it to follow AGENTS.md. Maybe, it need to be refined.

[koppor]

No. Use existing framework

[koppor]

No - https://github.com/JabRef/jabref/blob/main/jabsrv/src/main/java/org/jabref/http/server/command/CommandResource.java should be used

[sonthien22501]

Following our discussion regarding the previous PR, I have decided to close it and delete that codebase to ensure I fully understand every line I commit. I want to align strictly with the project's quality standards.

Current Progress: Instead of generating a new server implementation, I dug into the existing jabsrv module. I discovered that JabRef already has a robust HttpServerManager based on Grizzly.

I have successfully:

Located the existing server logic and identified why it wasn't starting (hidden preferences).

Enabled the server locally (port 6051) and verified the connection from a browser using the existing REST endpoints.

[koppor]

@sonthien22501 Nice. Its a learning path. No need to know everything right at the beginning. Its a journey. Aim is knowledge and experience growth.