Docs: rewrite prebuild-script migration guide around --combined-output

[dfed]

Summary

• The 2.x migration section in Documentation/Manual.md pointed prebuild-script migrants at generate --swift-manifest, but our own Bazel rule (bazel/safedi.bzl) and Tuist plugin (TuistPlugins/SafeDITuist/.../SafeDI.swift) use generate --combined-output --module-info-output instead — that flow produces a single statically-known output path, which is strictly simpler for any hand-written prebuild script
• Rewrites the migration section to lead with --combined-output: minimal single-module example, then a multi-module example that wires --module-info-output + --dependent-module-info-file-path for cross-module @Instantiable resolution
• Links to bazel/safedi.bzl and the Tuist plugin as canonical reference implementations
• Keeps --swift-manifest documented as the alternative for per-root output files, and notes the two emission modes are mutually exclusive
• Hardens SafeDITool's path-list CSV parsing: an echo "x.safedi" > deps.csv (as shown in the new docs) writes a trailing newline that previously survived components(separatedBy: ",") + removingEmpty() and got baked into the resolved file URL, failing the dependent-module load with a misleading file-not-found. A new String.parsedPathListCSV() helper now splits on commas/newlines and trims surrounding whitespace; applied to Generate's deps/sources/cache-check sites and Scan's sources site.

Test plan

• Render Documentation/Manual.md and confirm the new section flows correctly
• Confirm both internal links (bazel/safedi.bzl, TuistPlugins/SafeDITuist/ProjectDescriptionHelpers/SafeDI.swift) resolve on GitHub
• Sanity-check the multi-module shell snippet matches what the Bazel rule and Tuist plugin actually invoke
• New regression test run_combinedOutput_resolvesDependentModuleInfo_whenDepsCSVHasTrailingNewline fails on the pre-fix code (file-not-found on <uuid>.safedi\n) and passes after the helper change
• Full swift test --traits sourceBuild — 922 tests pass
• ./CLI/lint.sh clean

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (4b626d5) to head (f48779a).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #296   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           41        41           
  Lines         7043      7040    -3     
=========================================
- Hits          7043      7040    -3     

Files with missing lines	Coverage Δ
Sources/SafeDITool/GenerateCommand.swift	100.00% <100.00%> (ø)
Sources/SafeDITool/SafeDITool.swift	100.00% <100.00%> (ø)
Sources/SafeDITool/ScanCommand.swift	100.00% <100.00%> (ø)

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