feat(core): reorder includes and add FEDiscretization plus Gauss tuples

Partition metadata loads before DOF-based caches, new kernels and column
helpers wire into the load order, Gmsh leaves the default include graph, and
MPI docstrings describe kernel-less overloads plus internal-force hook.

- Add reference_gauss_tuples.jl and dof_based_pass1; include poroelastic and
  thermo_poroelastic kernels after thermo_elastic
- Hoist partitioning, halo_exchange, packed_layout, redundant_kernel_depwarn,
  ka_column_homogeneity, kernel_column ahead of dof_based_coo.jl
- Add physics/discretization.jl (FEDiscretization); drop gmsh_reader include
- Extend MPI matvec docstrings; declare mpi_partitioned_internal_force_owned!

src/physics/discretization.jl

@@ -0,0 +1,53 @@
+# SPDX-FileCopyrightText: 2015-2026 Jukka Aho
+# SPDX-License-Identifier: MIT
+
+"""
+    FEDiscretization(elements, handler, mesh, cache, assembler)
+
+Lightweight bundle of the usual DOF-based finite-element assembly inputs:
+`elements` from [`create_elements!`](@ref), the [`DOFHandler`](@ref), the
+[`AbstractMesh`](@ref), a pre-built [`DOFBasedCOOCache`](@ref) (whose
+[`kernel_column`](@ref) holds the volume kernel), and a
+[`DOFBasedCOOAssembler`](@ref) tag.
+
+Use [`assemble!`](@ref)`(fe)` then [`linear_system`](@ref)`(fe)` to obtain
+`(K, f)` without threading several separate variables through driver code.
+
+This is intentionally minimal: it does not own the mesh or elements, impose
+boundary conditions, or choose a solver. The kernel is read from
+`fe.cache.kernel_column` only; there is no separate redundant kernel field.
+"""
+struct FEDiscretization{E,H,M,C,A}
+    elements::Vector{E}
+    handler::H
+    mesh::M
+    cache::C
+    assembler::A
+end
+
+@inline function assemble!(fe::FEDiscretization; kwargs...)
+    return assemble!(fe.cache, fe.assembler, fe.mesh; kwargs...)
+end
+
+@inline function assemble_internal_force!(f::AbstractVector{Float64}, fe::FEDiscretization; kwargs...)
+    return assemble_internal_force!(f, fe.cache, fe.assembler, fe.mesh; kwargs...)
+end
+
+@inline function nonlinear_equilibrium_residual!(
+    r::AbstractVector{Float64},
+    f_ext::AbstractVector{Float64},
+    f_work::AbstractVector{Float64},
+    fe::FEDiscretization,
+    u::AbstractVector{Float64};
+    kwargs...,
+)
+    return nonlinear_equilibrium_residual!(
+        r, f_ext, f_work, fe.cache, fe.assembler, fe.mesh, u; kwargs...,
+    )
+end
+
+@inline function linear_system(fe::FEDiscretization)
+    return extract_system(fe.cache)
+end
+
+@inline total_dofs(fe::FEDiscretization) = fe.handler.total_dofs