Generate one output file per root @Instantiable

[dfed]

Summary

• Replace --dependency-tree-output (single file) with --swift-manifest (JSON manifest mapping input files to output files)
• One output file per @Instantiable(isRoot: true) root instead of a monolithic SafeDI.swift
• Introduce SafeDIToolManifest Codable type as the explicit contract between plugin/build systems and the tool
• Manifest uses an ordered array of InputOutputMap structs (not a dictionary) for concrete ordering and extensibility
• Plugin scans source files for roots, writes a manifest with relative input paths (for remote cache compatibility), and declares per-root output files
• Tool validates the manifest against parsed roots and writes to specified output paths
• Add sourceFilePath to Instantiable for tracking which file each root came from
• File header is written once per output file, even when multiple roots share a source file
• Document manifest format in Manual.md and migration steps in README

Motivation

1. Incremental compilation — when one root's dependency tree changes, only that root's generated file needs recompilation
2. Futureproofing — the manifest structure scales to additional output kinds (e.g. mock generation) without growing the CLI argument list

Test plan

• All 369 tests pass locally (swift test)
• Code coverage does not decrease (98.99% total)
• Lint passes (./lint.sh)
• Package integration builds locally
• Project integration builds locally
• CI passes

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.91%. Comparing base (27aaf91) to head (f6229a1).

Additional details and impacted files

@@                     Coverage Diff                     @@
##           dfed/major-version-bump     #202      +/-   ##
===========================================================
+ Coverage                    99.88%   99.91%   +0.03%     
===========================================================
  Files                           36       37       +1     
  Lines                         3452     3501      +49     
===========================================================
+ Hits                          3448     3498      +50     
+ Misses                           4        3       -1     

Files with missing lines	Coverage Δ
...afeDICore/Generators/DependencyTreeGenerator.swift	100.00% <100.00%> (ø)
Sources/SafeDICore/Models/InstantiableStruct.swift	100.00% <ø> (ø)
Sources/SafeDICore/Models/SafeDIToolManifest.swift	100.00% <100.00%> (ø)
Sources/SafeDITool/SafeDITool.swift	99.65% <100.00%> (-0.35%)	⬇️

... and 1 file with indirect coverage changes

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