Bump manifold pin + fold to single #1690 carry-patch (v0.4.0-alpha.1)

[zmerlynn]

Summary

Pre-release groundwork for v0.4.0. Pins manifold to current upstream master and replaces the three shim-side iostream patches with a single vendored diff of elalish/manifold#1690 — the upstream PR that adds MANIFOLD_NO_IOSTREAM natively. Once #1690 lands and the manifold pin moves past it, the carry-patch drops entirely and a v0.4.0 (non-alpha) release follows.

What changed

Helper refactor (cmake/WasmCxxShimManifold.cmake):

• Drops the Clipper2 pre-declaration. Manifold's manifoldDeps.cmake (post-#1690) owns the FetchContent_Declare(Clipper2 ...) and derives CLIPPER2_NO_IOSTREAM=ON from MANIFOLD_NO_IOSTREAM=ON automatically.
• Sets MANIFOLD_NO_IOSTREAM=ON as a CMake cache var; manifold's option chain propagates the macros as PUBLIC compile defs.
• API: removes CLIPPER2_GIT_TAG and EXTRA_CLIPPER2_PATCHES (manifold owns Clipper2 now). MANIFOLD_GIT_TAG / EXTRA_MANIFOLD_PATCHES / SKIP_BUILTIN_PATCHES continue to work.

Carry-patches:

• Three old patches (0001-clipper2-strip-iostream, 0002-manifold-ifdef-iostream, 0003-manifold-test-main-ifdef-filesystem) deleted.
• Single new patch 0001-manifold-no-iostream.patch — verbatim diff of #1690 against pinned upstream commit 5f95a3ac.

Test expansion: 71 → 121 tests run on the shim. Adds boolean_complex_test, manifoldc_test, smooth_test alongside existing boolean_test, cross_section_test, sdf_test. Skipped:

• hull_test, properties_test, samples_test — need the samples helper library (would also require pulling sample-geometry sources).
• manifold_test — uses std::set and threading constructs without direct <set>/<thread> includes, which our libcxx subset doesn't ship transitively.
• polygon_test — RegisterPolygonTests is no-op'd under MANIFOLD_NO_IOSTREAM, file would compile but contribute zero tests.

Size budget: manifold_tests_size_budget bumped 1.10 → 1.40 MB. Current ~1.07 MB; ~30% headroom for future test additions.

Test plan

• cmake --preset wasm32 -DWASM_CXX_SHIM_BUILD_MANIFOLD_LINK=ON && cmake --build --preset wasm32 && ctest --preset wasm32: 18/18 ctest entries pass.
• Inner harness count: 121 manifold tests pass.
• manifold-link-probe.wasm size: 339 KB (well under 450 KB budget).
• manifold-tests.wasm size: 1.07 MB (well under 1.40 MB budget).
• Both wasms have zero unexpected imports (manifold_link_imports_check + manifold_tests_imports_check).
• Helper API smoke test (wasm_cxx_shim_helper_api_smoke) updated for the new file layout.
• Idempotent re-config: cmake --build --preset wasm32 after editing a CMakeLists.txt file completes without re-applying the carry-patch (relies on a wrapper-script PATCH_COMMAND in #1690).

Notes for the (one-person) reviewer

• This is the "what the shim looks like once #1690 lands" preview. CI will pin to a specific upstream commit (5f95a3ac); if #1690 evolves in upstream review, this branch may need re-rolling (alpha.2, alpha.3, etc.).
• Tag (after merge): v0.4.0-alpha.1+5f95a3ac. The non-alpha v0.4.0 ships once #1690 actually merges and the manifold pin moves past it (drops the carry-patch, drops the +<sha> build-metadata).
• API breakage in the helper (dropped CLIPPER2_GIT_TAG / EXTRA_CLIPPER2_PATCHES) is fair game in a pre-1.0 alpha. CHANGELOG flags it.

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