CLI: enable Native AOT publish

[sjvrensburg]

Summary

Phase 2 of the AOT exploration. The CLI now produces a Native AOT binary on dotnet publish -c Release -r <rid>. End-to-end verified on linux-x64.

What changed

• <PublishAot>true</PublishAot> on RailReader2.Cli.csproj (replaces PublishSingleFile, which is incompatible).
• New CliJsonContext source-gen context covers StructureOutput, AnnotationExportOutput, VlmOutput, and shared output records.
• StructureCommand, AnnotationsCommand, VlmCommand switched to source-gen typed Serialize/Deserialize overloads.
• Shared.JsonOptions sets TypeInfoResolver = CliJsonContext.Default so future consumers of these options get the source-gen path automatically.

Surprises (good)

• OnnxRuntime, OpenAI, PDFium, SkiaSharp all AOT-clean as-is — no shims, no workarounds.
• Only fix needed was the CLI's own three JsonSerializer.Serialize<T> call sites.
• Output byte-identical between AOT and JIT.

Measurements (linux-x64)

	AOT	JIT
Main binary	12 MB	requires .NET runtime
Cold-start --help	6–37 ms	~500 ms (self-contained)
structure --analyze 2 pages incl. ONNX init	5.4s	15.2s

Not in scope

• CI workflow still uses JIT publish; an AOT release artifact target is a follow-up.
• Windows / macOS AOT publish not tested locally — the per-platform native libs should pick up automatically but each RID needs its own publish-and-test pass.

Test plan

• dotnet build RailReader2.slnx -c Release clean
• 281/281 tests pass
• dotnet publish -c Release -r linux-x64 succeeds with 0 warnings
• All 5 commands (render, structure, annotations, vlm, export) run end-to-end
• Structure JSON output byte-identical to JIT path

🤖 Generated with Claude Code