Fix headless stdout flooding

[travisformayor]

Running simulations through SynBioSuite can fail with ERR_CHILD_PROCESS_STDIO_MAXBUFFER when reb2sac progress output overflows Node.js's buffer in iBioSim-API. In headless mode, Run.java dumps every progress line (Time=X) to stdout, but nothing downstream uses them, they just accumulate until the buffer overflows.

• Skip System.out.println for lines successfully parsed as progress updates. Diagnostic output (warnings, errors) still prints.
• GUI path is unchanged, progress still goes through parent.send().
• Add explicit transitive deps to dataModels/pom.xml so the module builds standalone.
• Fix http to https for osgeo Maven repo URL.
• Ignore .sdkmanrc in .gitignore.

[Copilot]

Pull request overview

This PR reduces headless simulation failures caused by excessive child-process output by suppressing reb2sac progress-line printing in headless mode, while keeping GUI progress reporting unchanged. It also updates build/infra metadata so modules build more reliably and use secure repository URLs.

Changes:

• Suppress stdout printing of successfully parsed Time=... progress lines when running headless (no parent), while still printing non-progress diagnostics.
• Add explicit dependencies to dataModels/pom.xml to support standalone builds and update the osgeo repository URL to HTTPS.
• Ignore .sdkmanrc in .gitignore.

Reviewed changes

Copilot reviewed 2 out of 3 changed files in this pull request and generated 3 comments.

File	Description
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java	Avoids printing progress lines to stdout in headless mode to prevent buffer flooding.
dataModels/pom.xml	Adds explicit dependencies for standalone builds and switches osgeo repo URL to HTTPS.
.gitignore	Ignores .sdkmanrc.

Comments suppressed due to low confidence (1)

analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java:901

• Progress detection uses line.contains("Time") and then unconditionally attempts substring(line.indexOf('=') + 1, ...). If a non-progress diagnostic line contains the word "Time" but not the expected Time=... format, this will throw and e.printStackTrace() will emit a stack trace per line, which can still flood stderr in headless runs. Tighten the condition (e.g., require Time= prefix / regex with = present) and avoid printing full stack traces in this hot loop (log once or include the offending line in a concise message).

						  if (line.contains("Time")) {
							  time = Double.parseDouble(line.substring(line.indexOf('=') + 1, line.length()));
							  isProgress = true;
							  if (oldTime > time) {
								  runNum++;
							  }
							  oldTime = time;
							  time += (runNum * properties.getSimulationProperties().getTimeLimit());
							  double d = ((time * 100) / runTime);
							  String s = d + "";
							  double decimal = Double.parseDouble(s.substring(s.indexOf('.'), s.length()));
							  if (decimal >= 0.5) {
								  prog = (int) (Math.ceil(d));
							  } else {
								  prog = (int) (d);
							  }
						  }
					  }
					  catch (Exception e) {
						  e.printStackTrace();
					  }

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[travisformayor]

Responded to each copilot review comment, none of them require any code changes