Partial upgrade of libsedml, fixed cli plot bugs

[CodeByDrescher]

Summary

Two largely independent changes bundled together:

1. Bug fixes for SED-ML/CLI visual results (the user-visible motivation)
2. Partial upgrade of the embedded jlibsedml fork to support those fixes —
   package reorg into org.jlibsedml.components.*, SEDML→SedML naming,
   new first-class Axis and Plot abstractions, generic ListOf<T>,
   and a SedMLDataContainer facade with model-pruning support.

Bug fixes

Plot rendering (vcell-cli)

• Legend no longer eats the plot when a series has many curves — legend
  font now scales down (1pt per 100 chars of label, floor 8pt).
  Results2DLinePlot.java
• Series labels are now picked correctly — three-tier fallback
  (curve name → curve id → data-generator name/id) and explicit "Time"
  detection for the x-axis.
  PlottingDataExtractor.java
• Spatial results task-id collisions fixed — keys are now SId, not raw
  String.
  SpatialResultsConverter.java, ReorganizedSpatialResults.java

SED-ML import/export

• Variable constructor arg-order bug — XPath and task reference were
  swapped, producing wrong variable mappings in exported SED-ML.
  SEDMLExporter.java
• NPE when SBML symbol mapping is null — explicit loop replaces
  stream.toMap, which fails on null values.
  SedMLImporter.java
• Multi-application BioModels now import correctly — SBMLImporter
  is keyed by SimulationContext, not BioModel, so each application
  in a BioModel gets its own symbol table.
  SedMLImporter.java
• Preserve insertion order of imported models (LinkedHashMap).
• Clearer/findable errors during SED-ML import (explicit exceptions
  instead of silent failures). BiosimulationLog.java

Defensive fixes

• cbit.vcell.math.Variable — null-checks and identity-validation
  unified into rename(); constructor delegates so validation can't be
  bypassed.
• SEDMLChooserPanel — tolerates SED-ML where a task references a
  missing model/simulation rather than NPE-ing the dialog.
• Regex character-range typo ([a-zA-z…] → [a-zA-Z…]) flagged by
  GitHub Advanced Security in SedMLReader.

jlibsedml partial upgrade

The local jlibsedml fork was reorganised to support the fixes above
and to model SED-ML constructs that were previously missing.

Restructure (mechanical):

• Classes moved into org.jlibsedml.components.{model,output,task, simulation,algorithm,dataGenerator,listOfConstructs}.
• SEDML* → SedML* naming throughout (SedMLDocument, SedMLReader,
  SedMLWriter, SedMLImporter, SedMLUtil, SedMLTags, …).

New infrastructure:

• First-class Axis hierarchy (Axis, XAxis, YAxis, ZAxis,
  RightYAxis) with LINEAR/LOG10 type — needed for proper axis-label
  picking.
• Abstract Plot superclass with axis, legend, and dimension
  state; cloneable.
• Generic ListOf<T> with order-preserving storage, id-based
  lookup, recursive searchFor, and duplicate-id guard.
• SedMLDataContainer — facade wrapping a SedML plus namespace
  and file-path metadata. Adds pruneSedML() to remove dangling
  task/datagenerator/output references (with cascading cleanup of
  nested repeated-tasks) and findById convenience accessors.
• New Calculation interface; new Analysis simulation type.
• equals/hashCode on SedBase; clone() deep-copy on SedML
  and all components.

Test infrastructure

• SSIMComparisonTool — perceptual image comparison (Structural
  Similarity Index) replacing pixel-exact baseline matching for plot
• New Calculation interface; new Analysis simulation type.
• equals/hashCode on SedBase; clone() deep-copy on SedML
  and all components.

Test infrastructure

• SSIMComparisonTool — perceptual image comparison (Structural
  Similarity Index) replacing pixel-exact baseline matching for plot
  tests. A "Modified SSIM" variant applies a 5×5 Gaussian blur before
  the structure term to tolerate sub-pixel font/rendering differences.
  Threshold set to 0.90 MSSIM after iteration.
• New baseline PNGs: plot_result_0.png, plot_result_1.png,
  parabolic.png (replacing plot_0/1.png, Parabolic.png).
• TestComponents.java — first jlibsedml unit test, exercises
  Axis parsing through SedMLReader.

Test plan

• mvn test -Dgroups="Fast" passes
• SED-ML import/export integration tests
  (SEDML_VCML_IT, SEDML_SBML_IT, BSTS_IT)
• Spot-check legend rendering on a high-species-count BioModel
• Spot-check spatial results export end-to-end
• Re-comment the tmate debug step in .github/workflows/ci_cd.yml
  before merge

Risk

• The jlibsedml package reorg touches ~200 files but is largely
  mechanical; cross-module call sites have been adapted.
• The BioModel→SBMLImporter to SimulationContext→SBMLImporter
  change is a real semantic shift — worth a careful look at
  SedMLImporter callers in test runs.

[jcschaff]

fail early when SimulationContext doesn't have a SBMLSymbolMapping in the SedMLImporter. make SedMLImporter.getSBMLSymbolMapping(simContext) throw IllegalStateException("no SBML importer registered for sim context " + simContext)

[CodeByDrescher]

Note that issue #1673 was created to point out the flaws this PR leaves CLI mode in. Code is functional and passes all tests, but needs return work when priorities come around again.

[jcschaff]

looks good, refactor of VCML/SBML during sedml importing needed but beyond scope of this PR, see issue #1673