Update JAX & MLIR dependency chain to v0.4.28

[tzunghanjuang]

Context: We target at 0.4.28 instead of 0.4.30 because many bufferization passes are removed after this llvm commit.

Description of the Change: Mandatory Updates:

• Cmake
  • Remove MhloShapeOpsToStandard link
  • Add StablehloPasses
  • Add MhloQuantToIntConversion (This will be removed after 0.4.29)
  • EnzymeStatic-18 => EnzymeStatic-19
  • RunnerUtils.h requires Float16Bits.h link
• LLVM
  • setDataLayout must happen before code generation or they will use the default one. link
• MLIR
  • updateRootInPlace => modifyOpInPlace
  • startRootUpdate => startOpModification
  • finalizeRootUpdate => finalizeOpModification
  • The order of transformed mlir expressions is different and required fine-tuning for CHECK-DAGs.
  • Using rewriter's method to release MeasurementOps (Caused by LLVM commit-b840d2968391dd610b792a65133a1edc1bcc397c). link
  • Allow replaceTerminatorWithUnconditionalJumpToSuccessBlock to accept LLVM:br. (New LLVM/MLIR will reuse LLVM::UnreachableOp and use LLVM::br to reach it.)
• Frontend
  • jax.linear_util => jax.extend.linear_util link
  • jax_ctx.module_context.replace => jax_ctx.replace
  • gensym(jaxprs, suffix) => gensym(suffix) link
  • Move name_stack out of mlir.ModuleContext (functions like lower_jaxpr_to_fun is taking name_stack now). link.
  • Pass LoweringRuleContext.ModuleContext instead of LoweringRuleContext to jaxpr_subcomp
  • Patch new _sin_lowering and _cos_lowering with _nary_lower_hlo(sine/cosine).
  • Variable names (like %0 => %cst) and orders in FileCheck.

Deprecations/Warnings:

• MLIR
  • x.cast<T>() => mlir::cast<T>(x) link
  • x.dyn_cast<T>() => mlir::dyn_cast<T>(x) link
  • x.isa<T>() => mlir::isa<T>(x) link
• Enzyme
  • Add DCMAKE_POLICY_DEFAULT_CMP0116

Related GitHub Issues: https://github.com/PennyLaneAI/catalyst/issues/863 [sc-67111]

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 97.93%. Comparing base (d33a2a2) to head (c494836). Report is 1 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #931 +/- ## ========================================== + Coverage 97.90% 97.93% +0.03% ========================================== Files 73 73 Lines 10373 10338 -35 Branches 1186 1170 -16 ========================================== - Hits 10156 10125 -31 + Misses 172 170 -2 + Partials 45 43 -2 ```

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