Drop carry-patch, bump manifold pin past #1690 merge (v0.4.0)

[zmerlynn]

Summary

Manifold's MANIFOLD_NO_IOSTREAM build option is now upstream — elalish/manifold#1690 merged on 2026-05-04. The single vendored carry-patch shipped at v0.4.0-alpha.1 is no longer needed; manifold owns the option natively, and its manifoldDeps.cmake carries a Clipper2 tracking patch for AngusJohnson/Clipper2#1094 internally.

This is the v0.4.0 (non-alpha) release the alpha tag was tracking.

What changed

Removed:

• cmake/manifold-patches/0001-manifold-no-iostream.patch (and the now-empty directory).
• SKIP_BUILTIN_PATCHES argument from wasm_cxx_shim_add_manifold() (no builtin patches to skip). MANIFOLD_GIT_TAG and EXTRA_MANIFOLD_PATCHES continue to work.
• install(DIRECTORY .../manifold-patches ...) rule.

Changed:

• Default MANIFOLD_GIT_TAG bumped from 5f95a3ac (master pre-#1690) to 3ce9622b (master at release time, includes #1690 + one downstream commit).
• Helper smoke test (check-manifold-helper.cmake) updated for the new file layout.
• READMEs (test/manifold-link/, test/manifold-tests/) updated to reflect the post-merge state.
• CHANGELOG: new v0.4.0 row in the tested-combinations table; new ## v0.4.0 section.

Test plan

• ctest --preset wasm32: 18/18 pass with WASM_CXX_SHIM_BUILD_MANIFOLD_LINK=ON.
• Inner manifold-tests harness: 121/121 pass.
• Build clean with bumped pin (no patch applied, manifold's option chain does the work).
• manifold_link_imports_check + manifold_tests_imports_check still pass — zero unexpected imports.
• Doc-staleness sweep: zero references to manifold-patches/ or the deleted patch outside CHANGELOG/plan.md historical narrative.

Notes

• Net diff: 8 files, 876 lines removed (mostly the carry-patch), 83 added.
• Tag (after merge): v0.4.0 plain — no +<sha> build metadata since the carry-patch is gone and we're tracking master directly.
• manifold-csg can bump its wasm-cxx-shim dependency to v0.4.0 once this lands.

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