refactor: Comment out old basis and problem files incompatible with new API

Commented out files using AbstractBasis{dim}:
- basis/lagrange_generated.jl (449 lines, uses AbstractBasis{1/2/3})
- basis/nurbs_segment.jl (NSeg <: AbstractBasis{1})
- basis/nurbs_surface.jl (NSurf <: AbstractBasis{2})
- basis/nurbs_solid.jl (NSolid <: AbstractBasis{3})
- basis/math.jl (jacobian, grad functions use AbstractBasis{dim})
- elements/elements_lagrange.jl (Poi1 <: AbstractBasis{0})
- elements/integrate.jl (references NSeg, Poi1, old basis types)

Commented out problem files using old Element API:
- problems_heat.jl (uses Seg2, Tri3, Quad4, element.sfields)
- problems_truss.jl (uses Seg2, Poi1, element.sfields)
- problems_elasticity.jl (uses old element types, element.sfields)
- problems_dirichlet.jl (uses old API)
- problems_mortar.jl (uses old API)
- problems_mortar_3d.jl (uses old API)

Status after this commit:
- Package loads successfully ✓
- ~70% of functionality removed (intentional)
- All 43 tests fail (expected - old API incompatible)
- Next: Regenerate basis functions for Lagrange{T,P}
- Then: Rewrite math.jl, integrate.jl, rebuild problems

Rationale: Clean break from old Dict-based, type-unstable architecture.
New GPU-ready Element requires complete rebuild of dependent code.

src/JuliaFEM.jl

@@ -208,13 +208,19 @@ include("basis/vandermonde.jl")
 # Types have "Basis" suffix to avoid conflicts with topology types
 # E.g., Tri3Basis, Quad4Basis, etc. (not Tri3, Quad4 which are topology types)
 include("basis/lagrange_generator.jl")
-include("basis/lagrange_generated.jl")  # Auto-generated by scripts/generate_lagrange_basis.jl
+# OLD generated basis files - commented out during refactoring to new Lagrange{T,P} design
+# include("basis/lagrange_generated.jl")  # Auto-generated by scripts/generate_lagrange_basis.jl
+# TODO: Regenerate for new parametric Lagrange{T,P} architecture
 
 include("basis/nurbs.jl")
-include("basis/nurbs_segment.jl")
-include("basis/nurbs_surface.jl")
-include("basis/nurbs_solid.jl")
-include("basis/math.jl")
+# OLD NURBS basis files - commented out during AbstractBasis refactoring
+# These use AbstractBasis{dim} syntax which conflicts with new non-parametric AbstractBasis
+# include("basis/nurbs_segment.jl")  # NSeg <: AbstractBasis{1}
+# include("basis/nurbs_surface.jl")  # NSurf <: AbstractBasis{2}
+# include("basis/nurbs_solid.jl")    # NSolid <: AbstractBasis{3}
+# TODO: Rewrite for new AbstractBasis (non-parametric)
+# include("basis/math.jl")  # Uses AbstractBasis{dim} throughout (jacobian, grad, interpolate, etc.)
+# TODO: Rewrite math functions for new AbstractBasis
 
 # Consolidate FEMBase.jl into src/ (Phase 1 continued)
 # Order matters: fields → types → sparse → elements → integrate → problems → assembly
@@ -227,8 +233,8 @@ include("fembase_compat.jl")
 
 include("sparse/sparse.jl")          # SparseMatrixCOO, SparseVectorCOO
 include("elements/elements.jl")      # Element type and interface
-include("elements/elements_lagrange.jl")  # Lagrange element specifics
-include("elements/integrate.jl")     # Integration utilities
+# include("elements/elements_lagrange.jl")  # OLD - uses AbstractBasis{0} (Poi1)
+# include("elements/integrate.jl")     # OLD - references NSeg, Poi1, etc.
 include("assembly/problems.jl")      # Problem types
 include("assembly/assembly.jl")      # Assembly framework
 include("solvers/solvers_base.jl")   # Base solver types
@@ -245,19 +251,19 @@ include("graph/graph_ordering.jl")
 # using AbaqusReader  # Consolidated into src/readers.jl
 # using AsterReader   # Consolidated into src/readers.jl
 
-# Problem types
-include("problems_heat.jl")
-export Heat, PlaneHeat
-include("problems_truss.jl")
-export Truss
-include("problems_elasticity.jl")
-export Elasticity
+# Problem types (OLD - all reference old basis types like Seg2, Tri3, Poi1, etc.)
+# include("problems_heat.jl")
+# export Heat, PlaneHeat
+# include("problems_truss.jl")
+# export Truss
+# include("problems_elasticity.jl")
+# export Elasticity
 # include("materials_plasticity.jl")  # Requires ForwardDiff for automatic differentiation
 # export plastic_von_mises
-include("problems_dirichlet.jl")
-export Dirichlet
+# include("problems_dirichlet.jl")
+# export Dirichlet
 
-export assemble!, postprocess!
+# export assemble!, postprocess!
 
 # TODO: Consolidate vendor packages (FEMBeam, Mortar) later
 # Structural elements: beams
@@ -268,11 +274,11 @@ export assemble!, postprocess!
 # @reexport using MortarContact2D
 # @reexport using MortarContact2DAD
 
-include("problems_mortar.jl")
-include("problems_mortar_3d.jl")
-export calculate_normals, calculate_normals!, project_from_slave_to_master,
-   project_from_master_to_slave, Mortar, get_slave_elements,
-   get_polygon_clip
+# include("problems_mortar.jl")
+# include("problems_mortar_3d.jl")
+# export calculate_normals, calculate_normals!, project_from_slave_to_master,
+#    project_from_master_to_slave, Mortar, get_slave_elements,
+#    get_polygon_clip
 # include("io.jl")  # Requires HDF5 and LightXML - skip for minimal deps
 # export Xdmf, h5file, xmffile, xdmf_filter, new_dataitem, update_xdmf!, save!
 include("solvers.jl")