Remove autotools build system. (#2639)

41 files changed, 0 insertions, 2377 deletions

diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index dc23e2272..000000000
--- a/src/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ..
-srcdir = src
-
-include $(topdir)/Makefile.subdir
diff --git a/src/Makefile.am b/src/Makefile.am
deleted file mode 100644
index d29dcd172..000000000
--- a/src/Makefile.am
+++ /dev/null
@@ -1,864 +0,0 @@
-# LIBCVC4_VERSION (-version-info) is in the form current:revision:age
-#
-# current -
-#   increment if interfaces have been added, removed or changed
-# revision -
-#   increment if source code has changed
-#   set to zero if current is incremented
-# age -
-#   increment if interfaces have been added
-#   set to zero if interfaces have been removed
-#   or changed
-#
-LIBCVC4_VERSION = @CVC4_LIBRARY_VERSION@
-
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-D __STDC_LIMIT_MACROS \
-	-D __STDC_FORMAT_MACROS \
-	-I@builddir@ -I@srcdir@/include -I@srcdir@
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas -Wno-parentheses $(FLAG_VISIBILITY_HIDDEN)
-
-SUBDIRS = lib base options util expr smt_util prop/minisat prop/bvminisat . parser bindings main
-# The THEORIES list has been moved to Makefile.theories
-include @top_srcdir@/src/Makefile.theories
-
-lib_LTLIBRARIES = libcvc4.la
-
-libcvc4_la_LDFLAGS = \
-	-no-undefined \
-	-version-info $(LIBCVC4_VERSION)
-
-# This "tricks" automake into linking us as a C++ library (rather than
-# as a C library, which messes up exception handling support)
-nodist_EXTRA_libcvc4_la_SOURCES = dummy.cpp
-libcvc4_la_SOURCES = \
-	git_versioninfo.cpp \
-	api/cvc4cpp.h \
-	api/cvc4cppkind.h \
-	api/cvc4cpp.cpp \
-	context/backtrackable.h \
-	context/cddense_set.h \
-	context/cdhashmap.h \
-	context/cdhashmap_forward.h \
-	context/cdhashset.h \
-	context/cdhashset_forward.h \
-	context/cdinsert_hashmap.h \
-	context/cdinsert_hashmap_forward.h \
-	context/cdlist.h \
-	context/cdlist_forward.h \
-	context/cdmaybe.h \
-	context/cdo.h \
-	context/cdqueue.h \
-	context/cdtrail_queue.h \
-	context/context.cpp \
-	context/context.h \
-	context/context_mm.cpp \
-	context/context_mm.h \
-	decision/decision_attributes.h \
-	decision/decision_engine.cpp \
-	decision/decision_engine.h \
-	decision/decision_strategy.h \
-	decision/justification_heuristic.cpp \
-	decision/justification_heuristic.h \
-	preprocessing/assertion_pipeline.cpp \
-	preprocessing/assertion_pipeline.h \
-	preprocessing/passes/apply_substs.cpp \
-	preprocessing/passes/apply_substs.h \
-	preprocessing/passes/apply_to_const.cpp \
-	preprocessing/passes/apply_to_const.h \
-	preprocessing/passes/bool_to_bv.cpp \
-	preprocessing/passes/bool_to_bv.h \
-	preprocessing/passes/bv_abstraction.cpp \
-	preprocessing/passes/bv_abstraction.h \
-	preprocessing/passes/bv_ackermann.cpp \
-	preprocessing/passes/bv_ackermann.h \
-	preprocessing/passes/bv_eager_atoms.cpp \
-	preprocessing/passes/bv_eager_atoms.h \
-	preprocessing/passes/bv_gauss.cpp \
-	preprocessing/passes/bv_gauss.h \
-	preprocessing/passes/bv_intro_pow2.cpp \
-	preprocessing/passes/bv_intro_pow2.h \
-	preprocessing/passes/bv_to_bool.cpp \
-	preprocessing/passes/bv_to_bool.h \
-	preprocessing/passes/extended_rewriter_pass.cpp \
-	preprocessing/passes/extended_rewriter_pass.h \
-	preprocessing/passes/global_negate.cpp \
-	preprocessing/passes/global_negate.h \
-	preprocessing/passes/int_to_bv.cpp \
-	preprocessing/passes/int_to_bv.h \
-	preprocessing/passes/ite_removal.cpp \
-	preprocessing/passes/ite_removal.h \
-	preprocessing/passes/ite_simp.cpp \
-	preprocessing/passes/ite_simp.h \
-	preprocessing/passes/non_clausal_simp.cpp \
-	preprocessing/passes/non_clausal_simp.h \
-	preprocessing/passes/nl_ext_purify.cpp \
-	preprocessing/passes/nl_ext_purify.h \
-	preprocessing/passes/pseudo_boolean_processor.cpp \
-	preprocessing/passes/pseudo_boolean_processor.h \
-	preprocessing/passes/miplib_trick.cpp \
-	preprocessing/passes/miplib_trick.h \
-	preprocessing/passes/quantifier_macros.cpp \
-	preprocessing/passes/quantifier_macros.h \
-	preprocessing/passes/quantifiers_preprocess.cpp \
-	preprocessing/passes/quantifiers_preprocess.h \
-	preprocessing/passes/real_to_int.cpp \
-	preprocessing/passes/real_to_int.h \
-	preprocessing/passes/rewrite.cpp \
-	preprocessing/passes/rewrite.h \
-	preprocessing/passes/sep_skolem_emp.cpp \
-	preprocessing/passes/sep_skolem_emp.h \
-	preprocessing/passes/sort_infer.cpp \
-	preprocessing/passes/sort_infer.h \
-	preprocessing/passes/static_learning.cpp \
-	preprocessing/passes/static_learning.h \
-	preprocessing/passes/sygus_inference.cpp \
-	preprocessing/passes/sygus_inference.h \
-	preprocessing/passes/symmetry_breaker.cpp \
-	preprocessing/passes/symmetry_breaker.h \
-	preprocessing/passes/symmetry_detect.cpp \
-	preprocessing/passes/symmetry_detect.h \
-	preprocessing/passes/synth_rew_rules.cpp \
-	preprocessing/passes/synth_rew_rules.h \
-	preprocessing/passes/theory_preprocess.cpp \
-	preprocessing/passes/theory_preprocess.h \
-	preprocessing/passes/unconstrained_simplifier.cpp \
-	preprocessing/passes/unconstrained_simplifier.h \
-	preprocessing/preprocessing_pass.cpp \
-	preprocessing/preprocessing_pass.h \
-	preprocessing/preprocessing_pass_context.cpp \
-	preprocessing/preprocessing_pass_context.h \
-	preprocessing/preprocessing_pass_registry.cpp \
-	preprocessing/preprocessing_pass_registry.h \
-	preprocessing/util/ite_utilities.cpp \
-	preprocessing/util/ite_utilities.h \
-	printer/dagification_visitor.cpp \
-	printer/dagification_visitor.h \
-	printer/printer.cpp \
-	printer/printer.h \
-	printer/sygus_print_callback.cpp \
-	printer/sygus_print_callback.h \
-	printer/ast/ast_printer.cpp \
-	printer/ast/ast_printer.h \
-	printer/cvc/cvc_printer.cpp \
-	printer/cvc/cvc_printer.h \
-	printer/smt2/smt2_printer.cpp \
-	printer/smt2/smt2_printer.h \
-	printer/tptp/tptp_printer.cpp \
-	printer/tptp/tptp_printer.h \
-	proof/arith_proof.cpp \
-	proof/arith_proof.h \
-	proof/array_proof.cpp \
-	proof/array_proof.h \
-	proof/bitvector_proof.cpp \
-	proof/bitvector_proof.h \
-	proof/clause_id.h \
-	proof/cnf_proof.cpp \
-	proof/cnf_proof.h \
-	proof/lemma_proof.cpp \
-	proof/lemma_proof.h \
-	proof/lfsc_proof_printer.cpp \
-	proof/lfsc_proof_printer.h \
-	proof/proof.h \
-	proof/proof_manager.cpp \
-	proof/proof_manager.h \
-	proof/proof_output_channel.cpp \
-	proof/proof_output_channel.h \
-	proof/proof_utils.cpp \
-	proof/proof_utils.h \
-	proof/sat_proof.h \
-	proof/sat_proof_implementation.h \
-	proof/simplify_boolean_node.cpp \
-	proof/simplify_boolean_node.h \
-	proof/skolemization_manager.cpp \
-	proof/skolemization_manager.h \
-	proof/theory_proof.cpp \
-	proof/theory_proof.h \
-	proof/uf_proof.cpp \
-	proof/uf_proof.h \
-	proof/unsat_core.cpp \
-	proof/unsat_core.h \
-	prop/cadical.cpp \
-	prop/cadical.h \
-	prop/cnf_stream.cpp \
-	prop/cnf_stream.h \
-	prop/cryptominisat.cpp \
-	prop/cryptominisat.h \
-	prop/prop_engine.cpp \
-	prop/prop_engine.h \
-	prop/registrar.h \
-	prop/sat_solver.h \
-	prop/sat_solver_factory.cpp \
-	prop/sat_solver_factory.h \
-	prop/sat_solver_types.h \
-	prop/theory_proxy.cpp \
-	prop/theory_proxy.h \
-	smt/command.cpp \
-	smt/command.h \
-	smt/command_list.cpp \
-	smt/command_list.h \
-	smt/dump.cpp \
-	smt/dump.h \
-	smt/logic_exception.h \
-	smt/logic_request.cpp \
-	smt/logic_request.h \
-	smt/managed_ostreams.cpp \
-	smt/managed_ostreams.h \
-	smt/model.cpp \
-	smt/model.h \
-	smt/model_core_builder.cpp \
-	smt/model_core_builder.h \
-	smt/smt_engine.cpp \
-	smt/smt_engine.h \
-	smt/smt_engine_check_proof.cpp \
-	smt/smt_engine_scope.cpp \
-	smt/smt_engine_scope.h \
-	smt/smt_statistics_registry.cpp \
-	smt/smt_statistics_registry.h \
-	smt/term_formula_removal.cpp \
-	smt/term_formula_removal.h \
-	smt/update_ostream.h \
-	theory/assertion.cpp \
-	theory/assertion.h \
-	theory/atom_requests.cpp \
-	theory/atom_requests.h \
-	theory/care_graph.h \
-	theory/evaluator.cpp \
-	theory/evaluator.h \
-	theory/interrupted.h \
-	theory/logic_info.cpp \
-	theory/logic_info.h \
-	theory/output_channel.h \
-	theory/quantifiers_engine.cpp \
-	theory/quantifiers_engine.h \
-	theory/rep_set.cpp \
-	theory/rep_set.h \
-	theory/rewriter.cpp \
-	theory/rewriter.h \
-	theory/rewriter_attributes.h \
-	theory/shared_terms_database.cpp \
-	theory/shared_terms_database.h \
-	theory/sort_inference.cpp \
-	theory/sort_inference.h \
-	theory/substitutions.cpp \
-	theory/substitutions.h \
-	theory/subs_minimize.cpp \
-	theory/subs_minimize.h \
-	theory/term_registration_visitor.cpp \
-	theory/term_registration_visitor.h \
-	theory/theory.cpp \
-	theory/theory.h \
-	theory/theory_engine.cpp \
-	theory/theory_engine.h \
-	theory/theory_model.cpp \
-	theory/theory_model.h \
-	theory/theory_model_builder.cpp \
-	theory/theory_model_builder.h \
-	theory/theory_registrar.h \
-	theory/theory_test_utils.h \
-	theory/type_enumerator.h \
-	theory/type_set.cpp \
-	theory/type_set.h \
-	theory/valuation.cpp \
-	theory/valuation.h \
-	theory/arith/approx_simplex.cpp \
-	theory/arith/approx_simplex.h \
-	theory/arith/arith_ite_utils.cpp \
-	theory/arith/arith_ite_utils.h \
-	theory/arith/arith_msum.cpp \
-	theory/arith/arith_msum.h \
-	theory/arith/arith_rewriter.cpp \
-	theory/arith/arith_rewriter.h \
-	theory/arith/arith_static_learner.cpp \
-	theory/arith/arith_static_learner.h \
-	theory/arith/arith_utilities.h \
-	theory/arith/arithvar.cpp \
-	theory/arith/arithvar.h \
-	theory/arith/attempt_solution_simplex.cpp \
-	theory/arith/attempt_solution_simplex.h \
-	theory/arith/bound_counts.h \
-	theory/arith/callbacks.cpp \
-	theory/arith/callbacks.h \
-	theory/arith/congruence_manager.cpp \
-	theory/arith/congruence_manager.h \
-	theory/arith/constraint.cpp \
-	theory/arith/constraint.h \
-	theory/arith/constraint_forward.h \
-	theory/arith/cut_log.cpp \
-	theory/arith/cut_log.h \
-	theory/arith/delta_rational.cpp \
-	theory/arith/delta_rational.h \
-	theory/arith/dio_solver.cpp \
-	theory/arith/dio_solver.h \
-	theory/arith/dual_simplex.cpp \
-	theory/arith/dual_simplex.h \
-	theory/arith/error_set.cpp \
-	theory/arith/error_set.h \
-	theory/arith/fc_simplex.cpp \
-	theory/arith/fc_simplex.h \
-	theory/arith/infer_bounds.cpp \
-	theory/arith/infer_bounds.h \
-	theory/arith/linear_equality.cpp \
-	theory/arith/linear_equality.h \
-	theory/arith/matrix.cpp \
-	theory/arith/matrix.h \
-	theory/arith/nonlinear_extension.h \
-	theory/arith/nonlinear_extension.cpp \
-	theory/arith/normal_form.cpp \
-	theory/arith/normal_form.h\
-	theory/arith/partial_model.cpp \
-	theory/arith/partial_model.h \
-	theory/arith/simplex.cpp \
-	theory/arith/simplex.h \
-	theory/arith/simplex_update.cpp \
-	theory/arith/simplex_update.h \
-	theory/arith/soi_simplex.cpp \
-	theory/arith/soi_simplex.h \
-	theory/arith/tableau.cpp \
-	theory/arith/tableau.h \
-	theory/arith/tableau_sizes.cpp \
-	theory/arith/tableau_sizes.h \
-	theory/arith/theory_arith.cpp \
-	theory/arith/theory_arith.h \
-	theory/arith/theory_arith_private.cpp \
-	theory/arith/theory_arith_private.h \
-	theory/arith/theory_arith_private_forward.h \
-	theory/arith/theory_arith_type_rules.h \
-	theory/arith/type_enumerator.h \
-	theory/arrays/array_info.cpp \
-	theory/arrays/array_info.h \
-	theory/arrays/array_proof_reconstruction.cpp \
-	theory/arrays/array_proof_reconstruction.h \
-	theory/arrays/static_fact_manager.cpp \
-	theory/arrays/static_fact_manager.h \
-	theory/arrays/theory_arrays.cpp \
-	theory/arrays/theory_arrays.h \
-	theory/arrays/theory_arrays_rewriter.cpp \
-	theory/arrays/theory_arrays_rewriter.h \
-	theory/arrays/theory_arrays_type_rules.h \
-	theory/arrays/type_enumerator.h \
-	theory/arrays/union_find.cpp \
-	theory/arrays/union_find.h \
-	theory/booleans/circuit_propagator.cpp \
-	theory/booleans/circuit_propagator.h \
-	theory/booleans/theory_bool.cpp \
-	theory/booleans/theory_bool.h \
-	theory/booleans/theory_bool_rewriter.cpp \
-	theory/booleans/theory_bool_rewriter.h \
-	theory/booleans/theory_bool_type_rules.h \
-	theory/booleans/type_enumerator.h \
-	theory/builtin/theory_builtin.cpp \
-	theory/builtin/theory_builtin.h \
-	theory/builtin/theory_builtin_rewriter.cpp \
-	theory/builtin/theory_builtin_rewriter.h \
-	theory/builtin/theory_builtin_type_rules.h \
-	theory/builtin/type_enumerator.cpp \
-	theory/builtin/type_enumerator.h \
-	theory/bv/abstraction.cpp \
-	theory/bv/abstraction.h \
-	theory/bv/bitblast/aig_bitblaster.cpp \
-	theory/bv/bitblast/aig_bitblaster.h \
-	theory/bv/bitblast/bitblast_strategies_template.h \
-	theory/bv/bitblast/bitblast_utils.h \
-	theory/bv/bitblast/bitblaster.h \
-	theory/bv/bitblast/eager_bitblaster.cpp \
-	theory/bv/bitblast/eager_bitblaster.h \
-	theory/bv/bitblast/lazy_bitblaster.cpp \
-	theory/bv/bitblast/lazy_bitblaster.h \
-	theory/bv/bv_eager_solver.cpp \
-	theory/bv/bv_eager_solver.h \
-	theory/bv/bv_inequality_graph.cpp \
-	theory/bv/bv_inequality_graph.h \
-	theory/bv/bv_quick_check.cpp \
-	theory/bv/bv_quick_check.h \
-	theory/bv/bv_subtheory.h \
-	theory/bv/bv_subtheory_algebraic.cpp \
-	theory/bv/bv_subtheory_algebraic.h \
-	theory/bv/bv_subtheory_bitblast.cpp \
-	theory/bv/bv_subtheory_bitblast.h \
-	theory/bv/bv_subtheory_core.cpp \
-	theory/bv/bv_subtheory_core.h \
-	theory/bv/bv_subtheory_inequality.cpp \
-	theory/bv/bv_subtheory_inequality.h \
-	theory/bv/slicer.cpp \
-	theory/bv/slicer.h \
-	theory/bv/theory_bv.cpp \
-	theory/bv/theory_bv.h \
-	theory/bv/theory_bv_rewrite_rules.h \
-	theory/bv/theory_bv_rewrite_rules_constant_evaluation.h \
-	theory/bv/theory_bv_rewrite_rules_core.h \
-	theory/bv/theory_bv_rewrite_rules_normalization.h \
-	theory/bv/theory_bv_rewrite_rules_operator_elimination.h \
-	theory/bv/theory_bv_rewrite_rules_simplification.h \
-	theory/bv/theory_bv_rewriter.cpp \
-	theory/bv/theory_bv_rewriter.h \
-	theory/bv/theory_bv_type_rules.h \
-	theory/bv/theory_bv_utils.cpp \
-	theory/bv/theory_bv_utils.h \
-	theory/bv/type_enumerator.h \
-	theory/datatypes/datatypes_rewriter.cpp \
-	theory/datatypes/datatypes_rewriter.h \
-	theory/datatypes/datatypes_sygus.cpp \
-	theory/datatypes/datatypes_sygus.h \
-	theory/datatypes/theory_datatypes.cpp \
-	theory/datatypes/theory_datatypes.h \
-	theory/datatypes/theory_datatypes_type_rules.h \
-	theory/datatypes/type_enumerator.cpp \
-	theory/datatypes/type_enumerator.h \
-	theory/datatypes/sygus_simple_sym.cpp \
-	theory/datatypes/sygus_simple_sym.h \
-	theory/decision_manager.cpp \
-	theory/decision_manager.h \
-	theory/decision_strategy.cpp \
-	theory/decision_strategy.h \
-	theory/ext_theory.cpp \
-	theory/ext_theory.h \
-	theory/fp/theory_fp.cpp \
-	theory/fp/theory_fp.h \
-	theory/fp/theory_fp_rewriter.cpp \
-	theory/fp/theory_fp_rewriter.h \
-	theory/fp/theory_fp_type_rules.h \
-	theory/fp/type_enumerator.h \
-	theory/fp/fp_converter.h \
-	theory/fp/fp_converter.cpp \
-	theory/idl/idl_assertion.cpp \
-	theory/idl/idl_assertion.h \
-	theory/idl/idl_assertion_db.cpp \
-	theory/idl/idl_assertion_db.h \
-	theory/idl/idl_model.cpp \
-	theory/idl/idl_model.h \
-	theory/idl/theory_idl.cpp \
-	theory/idl/theory_idl.h \
-	theory/quantifiers/alpha_equivalence.cpp \
-	theory/quantifiers/alpha_equivalence.h \
-	theory/quantifiers/anti_skolem.cpp \
-	theory/quantifiers/anti_skolem.h \
-	theory/quantifiers/bv_inverter.cpp \
-	theory/quantifiers/bv_inverter.h \
-	theory/quantifiers/bv_inverter_utils.cpp \
-	theory/quantifiers/bv_inverter_utils.h \
-	theory/quantifiers/candidate_rewrite_database.cpp \
-	theory/quantifiers/candidate_rewrite_database.h \
-	theory/quantifiers/candidate_rewrite_filter.cpp \
-	theory/quantifiers/candidate_rewrite_filter.h \
-	theory/quantifiers/cegqi/ceg_instantiator.cpp \
-	theory/quantifiers/cegqi/ceg_instantiator.h \
-	theory/quantifiers/cegqi/ceg_arith_instantiator.cpp \
-	theory/quantifiers/cegqi/ceg_arith_instantiator.h \
-	theory/quantifiers/cegqi/ceg_bv_instantiator.cpp \
-	theory/quantifiers/cegqi/ceg_bv_instantiator.h \
-	theory/quantifiers/cegqi/ceg_bv_instantiator_utils.cpp \
-	theory/quantifiers/cegqi/ceg_bv_instantiator_utils.h \
-	theory/quantifiers/cegqi/ceg_dt_instantiator.cpp \
-	theory/quantifiers/cegqi/ceg_dt_instantiator.h \
-	theory/quantifiers/cegqi/ceg_epr_instantiator.cpp \
-	theory/quantifiers/cegqi/ceg_epr_instantiator.h \
-	theory/quantifiers/cegqi/inst_strategy_cegqi.cpp \
-	theory/quantifiers/cegqi/inst_strategy_cegqi.h \
-	theory/quantifiers/conjecture_generator.cpp \
-	theory/quantifiers/conjecture_generator.h \
-	theory/quantifiers/dynamic_rewrite.cpp \
-	theory/quantifiers/dynamic_rewrite.h \
-	theory/quantifiers/ematching/candidate_generator.cpp \
-	theory/quantifiers/ematching/candidate_generator.h \
-	theory/quantifiers/ematching/ho_trigger.cpp \
-	theory/quantifiers/ematching/ho_trigger.h \
-	theory/quantifiers/ematching/inst_match_generator.cpp \
-	theory/quantifiers/ematching/inst_match_generator.h \
-	theory/quantifiers/ematching/inst_strategy_e_matching.cpp \
-	theory/quantifiers/ematching/inst_strategy_e_matching.h \
-	theory/quantifiers/ematching/instantiation_engine.cpp \
-	theory/quantifiers/ematching/instantiation_engine.h \
-	theory/quantifiers/ematching/trigger.cpp \
-	theory/quantifiers/ematching/trigger.h \
-	theory/quantifiers/equality_query.cpp \
-	theory/quantifiers/equality_query.h \
-	theory/quantifiers/equality_infer.cpp \
-	theory/quantifiers/equality_infer.h \
-	theory/quantifiers/expr_miner.cpp \
-	theory/quantifiers/expr_miner.h \
-	theory/quantifiers/expr_miner_manager.cpp \
-	theory/quantifiers/expr_miner_manager.h \
-	theory/quantifiers/extended_rewrite.cpp \
-	theory/quantifiers/extended_rewrite.h \
-	theory/quantifiers/first_order_model.cpp \
-	theory/quantifiers/first_order_model.h \
-	theory/quantifiers/fmf/ambqi_builder.cpp \
-	theory/quantifiers/fmf/ambqi_builder.h \
-	theory/quantifiers/fmf/bounded_integers.cpp \
-	theory/quantifiers/fmf/bounded_integers.h \
-	theory/quantifiers/fmf/full_model_check.cpp \
-	theory/quantifiers/fmf/full_model_check.h \
-	theory/quantifiers/fmf/model_builder.cpp \
-	theory/quantifiers/fmf/model_builder.h \
-	theory/quantifiers/fmf/model_engine.cpp \
-	theory/quantifiers/fmf/model_engine.h \
-	theory/quantifiers/fun_def_process.cpp \
-	theory/quantifiers/fun_def_process.h \
-	theory/quantifiers/instantiate.cpp \
-	theory/quantifiers/instantiate.h \
-	theory/quantifiers/inst_match.cpp \
-	theory/quantifiers/inst_match.h \
-	theory/quantifiers/inst_match_trie.cpp \
-	theory/quantifiers/inst_match_trie.h \
-	theory/quantifiers/inst_propagator.cpp \
-	theory/quantifiers/inst_propagator.h \
-	theory/quantifiers/inst_strategy_enumerative.cpp \
-	theory/quantifiers/inst_strategy_enumerative.h \
-	theory/quantifiers/lazy_trie.cpp \
-	theory/quantifiers/lazy_trie.h \
-	theory/quantifiers/local_theory_ext.cpp \
-	theory/quantifiers/local_theory_ext.h \
-	theory/quantifiers/quant_conflict_find.cpp \
-	theory/quantifiers/quant_conflict_find.h \
-	theory/quantifiers/quant_epr.cpp \
-	theory/quantifiers/quant_epr.h \
-	theory/quantifiers/quant_relevance.cpp \
-	theory/quantifiers/quant_relevance.h \
-	theory/quantifiers/quant_split.cpp \
-	theory/quantifiers/quant_split.h \
-	theory/quantifiers/quant_util.cpp \
-	theory/quantifiers/quant_util.h \
-	theory/quantifiers/quantifiers_attributes.cpp \
-	theory/quantifiers/quantifiers_attributes.h \
-	theory/quantifiers/quantifiers_rewriter.cpp \
-	theory/quantifiers/quantifiers_rewriter.h \
-	theory/quantifiers/query_generator.cpp \
-	theory/quantifiers/query_generator.h \
-	theory/quantifiers/relevant_domain.cpp \
-	theory/quantifiers/relevant_domain.h \
-	theory/quantifiers/rewrite_engine.cpp \
-	theory/quantifiers/rewrite_engine.h \
-	theory/quantifiers/single_inv_partition.cpp \
-	theory/quantifiers/single_inv_partition.h \
-	theory/quantifiers/skolemize.cpp \
-	theory/quantifiers/skolemize.h \
-	theory/quantifiers/sygus/cegis.cpp \
-	theory/quantifiers/sygus/cegis.h \
-	theory/quantifiers/sygus/cegis_unif.cpp \
-	theory/quantifiers/sygus/cegis_unif.h \
-	theory/quantifiers/sygus/ce_guided_single_inv.cpp \
-	theory/quantifiers/sygus/ce_guided_single_inv.h \
-	theory/quantifiers/sygus/enum_stream_substitution.cpp \
-	theory/quantifiers/sygus/enum_stream_substitution.h \
-	theory/quantifiers/sygus/sygus_pbe.cpp \
-	theory/quantifiers/sygus/sygus_pbe.h \
-	theory/quantifiers/sygus/ce_guided_single_inv_sol.cpp \
-	theory/quantifiers/sygus/ce_guided_single_inv_sol.h \
-	theory/quantifiers/sygus/sygus_eval_unfold.cpp \
-	theory/quantifiers/sygus/sygus_eval_unfold.h \
-	theory/quantifiers/sygus/sygus_explain.cpp \
-	theory/quantifiers/sygus/sygus_explain.h \
-	theory/quantifiers/sygus/sygus_invariance.cpp \
-	theory/quantifiers/sygus/sygus_invariance.h \
-	theory/quantifiers/sygus/sygus_grammar_cons.cpp \
-	theory/quantifiers/sygus/sygus_grammar_cons.h \
-	theory/quantifiers/sygus/sygus_grammar_norm.cpp \
-	theory/quantifiers/sygus/sygus_grammar_norm.h \
-	theory/quantifiers/sygus/sygus_grammar_red.cpp \
-	theory/quantifiers/sygus/sygus_grammar_red.h \
-	theory/quantifiers/sygus/sygus_module.cpp \
-	theory/quantifiers/sygus/sygus_module.h \
-	theory/quantifiers/sygus/sygus_process_conj.cpp \
-	theory/quantifiers/sygus/sygus_process_conj.h \
-	theory/quantifiers/sygus/sygus_repair_const.cpp \
-	theory/quantifiers/sygus/sygus_repair_const.h \
-	theory/quantifiers/sygus/sygus_unif.cpp \
-	theory/quantifiers/sygus/sygus_unif.h \
-	theory/quantifiers/sygus/sygus_unif_io.cpp \
-	theory/quantifiers/sygus/sygus_unif_io.h \
-	theory/quantifiers/sygus/sygus_unif_rl.cpp \
-	theory/quantifiers/sygus/sygus_unif_rl.h \
-	theory/quantifiers/sygus/sygus_unif_strat.cpp \
-	theory/quantifiers/sygus/sygus_unif_strat.h \
-	theory/quantifiers/sygus/synth_conjecture.cpp \
-	theory/quantifiers/sygus/synth_conjecture.h \
-	theory/quantifiers/sygus/synth_engine.cpp \
-	theory/quantifiers/sygus/synth_engine.h \
-	theory/quantifiers/sygus/term_database_sygus.cpp \
-	theory/quantifiers/sygus/term_database_sygus.h \
-	theory/quantifiers/sygus_sampler.cpp \
-	theory/quantifiers/sygus_sampler.h \
-	theory/quantifiers/term_canonize.cpp \
-	theory/quantifiers/term_canonize.h \
-	theory/quantifiers/term_database.cpp \
-	theory/quantifiers/term_database.h \
-	theory/quantifiers/term_enumeration.cpp \
-	theory/quantifiers/term_enumeration.h \
-	theory/quantifiers/term_util.cpp \
-	theory/quantifiers/term_util.h \
-	theory/quantifiers/theory_quantifiers.cpp \
-	theory/quantifiers/theory_quantifiers.h \
-	theory/quantifiers/theory_quantifiers_type_rules.h \
-	theory/sep/theory_sep.cpp \
-	theory/sep/theory_sep.h \
-	theory/sep/theory_sep_rewriter.cpp \
-	theory/sep/theory_sep_rewriter.h \
-	theory/sep/theory_sep_type_rules.h \
-	theory/sets/normal_form.h \
-	theory/sets/rels_utils.h \
-	theory/sets/theory_sets.cpp \
-	theory/sets/theory_sets.h \
-	theory/sets/theory_sets_private.cpp \
-	theory/sets/theory_sets_private.h \
-	theory/sets/theory_sets_rels.cpp \
-	theory/sets/theory_sets_rels.h \
-	theory/sets/theory_sets_rewriter.cpp \
-	theory/sets/theory_sets_rewriter.h \
-	theory/sets/theory_sets_type_enumerator.h \
-	theory/sets/theory_sets_type_rules.h \
-	theory/strings/regexp_elim.cpp \
-	theory/strings/regexp_elim.h \
-	theory/strings/regexp_operation.cpp \
-	theory/strings/regexp_operation.h \
-	theory/strings/skolem_cache.cpp \
-	theory/strings/skolem_cache.h \
-	theory/strings/theory_strings.cpp \
-	theory/strings/theory_strings.h \
-	theory/strings/theory_strings_preprocess.cpp \
-	theory/strings/theory_strings_preprocess.h \
-	theory/strings/theory_strings_rewriter.cpp \
-	theory/strings/theory_strings_rewriter.h \
-	theory/strings/theory_strings_type_rules.h \
-	theory/strings/type_enumerator.h \
-	theory/uf/equality_engine.cpp \
-	theory/uf/equality_engine.h \
-	theory/uf/equality_engine_types.h \
-	theory/uf/symmetry_breaker.cpp \
-	theory/uf/symmetry_breaker.h \
-	theory/uf/theory_uf.cpp \
-	theory/uf/theory_uf.h \
-	theory/uf/theory_uf_model.cpp \
-	theory/uf/theory_uf_model.h \
-	theory/uf/theory_uf_rewriter.h \
-	theory/uf/theory_uf_strong_solver.cpp \
-	theory/uf/theory_uf_strong_solver.h \
-	theory/uf/theory_uf_type_rules.h
-
-nodist_libcvc4_la_SOURCES = \
-	theory/rewriter_tables.h \
-	theory/theory_traits.h \
-	theory/type_enumerator.cpp
-
-libcvc4_la_LIBADD = \
-	@builddir@/base/libbase.la \
-	@builddir@/options/liboptions.la \
-	@builddir@/util/libutil.la \
-	@builddir@/expr/libexpr.la \
-	@builddir@/smt_util/libsmtutil.la \
-	@builddir@/prop/minisat/libminisat.la \
-	@builddir@/prop/bvminisat/libbvminisat.la
-if CVC4_PROOF
-libcvc4_la_LIBADD += \
-	@top_builddir@/proofs/signatures/libsignatures.la
-endif
-
-libcvc4_la_LIBADD += \
-	@builddir@/lib/libreplacements.la
-
-if CVC4_USE_GLPK
-libcvc4_la_LIBADD += $(GLPK_LIBS)
-libcvc4_la_LDFLAGS += $(GLPK_LDFLAGS)
-endif
-
-if CVC4_USE_ABC
-libcvc4_la_LIBADD += $(ABC_LIBS)
-libcvc4_la_LDFLAGS += $(ABC_LDFLAGS)
-endif
-
-if CVC4_USE_CADICAL
-libcvc4_la_LIBADD += $(CADICAL_LIBS)
-libcvc4_la_LDFLAGS += $(CADICAL_LDFLAGS)
-endif
-
-if CVC4_USE_CRYPTOMINISAT
-libcvc4_la_LIBADD += $(CRYPTOMINISAT_LIBS)
-libcvc4_la_LDFLAGS += $(CRYPTOMINISAT_LDFLAGS)
-endif
-
-if CVC4_USE_LFSC
-libcvc4_la_LIBADD += $(LFSC_LIBS)
-libcvc4_la_LDFLAGS += $(LFSC_LDFLAGS)
-endif
-
-
-
-BUILT_SOURCES = \
-	theory/rewriter_tables.h \
-	theory/theory_traits.h \
-	theory/type_enumerator.cpp \
-	$(top_builddir)/src/.subdirs
-
-CLEANFILES = \
-	git_versioninfo.cpp \
-	gitinfo.tmp \
-	gitinfo \
-	theory/rewriter_tables.h \
-	theory/theory_traits.h \
-	theory/type_enumerator.cpp \
-	$(top_builddir)/src/.subdirs
-
-EXTRA_DIST = \
-	Makefile.theories \
-	cvc4.i \
-	include/cvc4.h \
-	include/cvc4_private.h \
-	include/cvc4_private_library.h \
-	include/cvc4_public.h \
-	include/cvc4parser_private.h \
-	include/cvc4parser_public.h \
-	mksubdirs \
-	smt/command.i \
-	smt/logic_exception.i \
-	smt/smt_engine.i \
-	proof/unsat_core.i \
-	theory/arith/kinds \
-	theory/arrays/kinds \
-	theory/booleans/kinds \
-	theory/builtin/kinds \
-	theory/bv/kinds \
-	theory/datatypes/kinds \
-	theory/example/ecdata.cpp \
-	theory/example/ecdata.h \
-	theory/example/theory_uf_tim.cpp \
-	theory/example/theory_uf_tim.h \
-	theory/fp/kinds \
-	theory/idl/kinds \
-	theory/logic_info.i \
-	theory/mkrewriter \
-	theory/mktheorytraits \
-	theory/quantifiers/kinds \
-	theory/rewriter_tables_template.h \
-	theory/sep/kinds \
-	theory/sets/kinds \
-	theory/strings/kinds \
-	theory/theory_traits_template.h \
-	theory/type_enumerator_template.cpp \
-	theory/uf/kinds
-
-git_versioninfo.cpp: gitinfo
-	$(AM_V_GEN)( \
-	  if test -s gitinfo; then \
-	    isgit=true; \
-	    branch=`head -1 gitinfo`; \
-	    rev=`head -2 gitinfo | tail -1 | awk '{print$$1}'`; \
-	    mods=`grep '^Modifications: ' gitinfo | awk '{print$$2} END { if(!NR) print "false" }'`; \
-	  else \
-	    isgit=false; \
-	    branch=unknown; \
-	    rev=unknown; \
-	    mods=false; \
-	  fi; \
-	  echo "#include \"base/configuration.h\""; \
-	  echo "const bool ::CVC4::Configuration::IS_GIT_BUILD = $$isgit;"; \
-	  echo "const char* const ::CVC4::Configuration::GIT_BRANCH_NAME = \"$$branch\";"; \
-	  echo "const char* const ::CVC4::Configuration::GIT_COMMIT = \"$$rev\";"; \
-	  echo "const bool ::CVC4::Configuration::GIT_HAS_MODIFICATIONS = $$mods;"; \
-	) >"$@"
-# This .tmp business is to keep from having to re-compile options.cpp
-# (and then re-link the libraries) if nothing has changed.
-gitinfo: gitinfo.tmp
-	$(AM_V_GEN)if diff -q gitinfo.tmp gitinfo &>/dev/null; then rm -f gitinfo.tmp; else mv gitinfo.tmp gitinfo; fi || true
-# .PHONY ensures the .tmp version is always rebuilt (to check for any changes)
-.PHONY: gitinfo.tmp
-gitinfo.tmp:
-	$(AM_V_GEN)(cd "$(top_srcdir)"; if test -e .git/HEAD; then if ! grep -q '^ref: refs/heads/' .git/HEAD; then echo; fi; sed 's,^ref: refs/heads/,,' .git/HEAD; git show-ref refs/heads/`sed 's,^ref: refs/heads/,,' .git/HEAD`; echo "Modifications: `test -z \"\`git status -s -uno\`\" && echo false || echo true`"; fi) >"$@" 2>/dev/null || true
-
-install-data-local:
-	(echo include/cvc4.h; \
-	 echo include/cvc4_public.h; \
-	 echo include/cvc4parser_public.h; \
-	 echo util/floatingpoint.h; \
-	 echo util/integer.h; \
-	 echo util/rational.h; \
-	 find * -name '*.h' | \
-		xargs grep -l '^# *include  *"cvc4.*_public\.h"'; \
-	(cd "$(srcdir)" && find * -name '*.h' | \
-		xargs grep -l '^# *include  *"cvc4.*_public\.h"')) | \
-	while read f; do \
-		if expr "$$f" : ".*_\(template\|private\|private_library\|test_utils\)\.h$$" &>/dev/null; then \
-			continue; \
-		fi; \
-		d="$$(echo "$$f" | sed 's,^include/,,')"; \
-		$(mkinstalldirs) "$$(dirname "$(DESTDIR)$(includedir)/cvc4/$$d")"; \
-		if [ -e "$$f" ]; then \
-			path="$$f"; \
-		else \
-			path="$(srcdir)/$$f"; \
-		fi; \
-		fixpath="$(top_builddir)/header_install.fix"; \
-		sed 's,^\([ \t]*#[ \t]*include[ \t*]\)"\(.*\)"\([ \t]*\)$$,\1<cvc4/\2>\3,' "$$path" > "$$fixpath" || exit 1; \
-		echo $(INSTALL_DATA) "$$fixpath" "$(DESTDIR)$(includedir)/cvc4/$$d"; \
-		if $(INSTALL_DATA) "$$fixpath" "$(DESTDIR)$(includedir)/cvc4/$$d"; then \
-			rm -f "$$fixpath"; \
-		else \
-			rm -f "$$fixpath"; \
-			exit 1; \
-		fi; \
-	done
-
-uninstall-local:
-	-(echo include/cvc4.h; \
-	  echo include/cvc4_public.h; \
-	  echo include/cvc4parser_public.h; \
-	  echo util/floatingpoint.h; \
-	  echo util/integer.h; \
-	  echo util/rational.h; \
-	  find * -name '*.h' | \
-		xargs grep -l '^# *include  *"cvc4.*_public\.h"'; \
-	(cd "$(srcdir)" && find * -name '*.h' | \
-		xargs grep -l '^# *include  *"cvc4.*_public\.h"')) | \
-	while read f; do \
-		if expr "$$f" : ".*_\(template\|private\|private_library\|test_utils\)\.h$$" &>/dev/null; then \
-			continue; \
-		fi; \
-		d="$$(echo "$$f" | sed 's,^include/,,')"; \
-		rm -f "$(DESTDIR)$(includedir)/cvc4/$$d"; \
-	done
-	-rmdir "$(DESTDIR)$(includedir)/cvc4/bindings"
-	-rmdir "$(DESTDIR)$(includedir)/cvc4"
-	-rmdir "$(DESTDIR)$(libdir)/ocaml/cvc4"
-
-# This rule is ugly.  It's needed to ensure that automake's dependence
-# includes are available during distclean, even though they come from
-# directories that are cleaned first.  Without this rule, "distclean"
-# fails.
-%.Plo:; $(MKDIR_P) "$(dir $@)" && : > "$@"
-
-#include @top_srcdir@/src/theory/Makefile.subdirs
-$(top_builddir)/src/.subdirs: $(top_srcdir)/src/Makefile.theories  @top_srcdir@/src/mksubdirs
-	$(AM_V_at)test -d $(top_builddir)/src || mkdir $(top_builddir)/src
-	$(AM_V_at)chmod +x @top_srcdir@/src/mksubdirs
-	$(AM_V_at)( @top_srcdir@/src/mksubdirs "$(top_srcdir)" ) > $(top_builddir)/src/.subdirs.tmp
-	@if ! diff -q $(top_builddir)/src/.subdirs $(top_builddir)/src/.subdirs.tmp &>/dev/null; then \
-		echo "  GEN   " $@; \
-		$(am__mv) $(top_builddir)/src/.subdirs.tmp $(top_builddir)/src/.subdirs; \
-	fi
-
-theory/rewriter_tables.h: theory/rewriter_tables_template.h theory/mkrewriter @top_builddir@/src/.subdirs @top_srcdir@/src/theory/*/kinds
-	$(AM_V_at)test -d $(top_builddir)/src/theory || mkdir -p @top_builddir@/src/theory
-	$(AM_V_at)chmod +x @srcdir@/theory/mkrewriter
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/theory/mkrewriter \
-		$< \
-		`cat @top_builddir@/src/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-theory/theory_traits.h: theory/theory_traits_template.h theory/mktheorytraits @top_builddir@/src/.subdirs @top_srcdir@/src/theory/*/kinds
-	$(AM_V_at)test -d $(top_builddir)/src/theory || mkdir -p @top_builddir@/src/theory
-	$(AM_V_at)chmod +x @srcdir@/theory/mktheorytraits
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/theory/mktheorytraits \
-		$< \
-		`cat @top_builddir@/src/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-theory/type_enumerator.cpp: theory/type_enumerator_template.cpp theory/mktheorytraits @top_builddir@/src/.subdirs @top_srcdir@/src/theory/*/kinds
-	$(AM_V_at)test -d $(top_builddir)/src/theory || mkdir -p @top_builddir@/src/theory
-	$(AM_V_at)chmod +x @srcdir@/theory/mktheorytraits
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/theory/mktheorytraits \
-		$< \
-		`cat @top_builddir@/src/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
diff --git a/src/Makefile.theories b/src/Makefile.theories
deleted file mode 100644
index 276663cc5..000000000
--- a/src/Makefile.theories
+++ /dev/null
@@ -1,3 +0,0 @@
-
-
-THEORIES = builtin booleans uf arith bv fp arrays datatypes sep sets strings quantifiers idl
diff --git a/src/base/Makefile.am b/src/base/Makefile.am
deleted file mode 100644
index 3706f57a3..000000000
--- a/src/base/Makefile.am
+++ /dev/null
@@ -1,77 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = libbase.la
-
-# Do not list built sources here!
-# Rather, list them under BUILT_SOURCES, and their .in versions under
-# EXTRA_DIST.  Otherwise, they're packaged up in the tarball, which is
-# no good---they belong in the configured builds/ directory.  If they
-# end up in the source directory, they build the cvc4 that was
-# configured at the time of the "make dist", which (1) may not be the
-# configuration that the user wants, and (2) might cause link errors.
-libbase_la_SOURCES = \
-	Makefile.am \
-	Makefile.in \
-	configuration.cpp \
-	configuration.h \
-	configuration_private.h \
-	cvc4_assert.cpp \
-	cvc4_assert.h \
-	cvc4_check.cpp \
-	cvc4_check.h \
-	exception.cpp \
-	exception.h \
-	listener.cpp \
-	listener.h \
-	map_util.h \
-	modal_exception.h \
-	output.cpp \
-	output.h
-
-# listing {Debug,Trace}_tags too ensures that make doesn't auto-remove it
-# after building (if it does, we don't get the "cached" effect with
-# the .tmp files below, and we have to re-compile and re-link each
-# time, even when there are no changes).
-BUILT_SOURCES = \
-	Debug_tags.h \
-	Debug_tags \
-	Trace_tags.h \
-	Trace_tags
-
-MOSTLYCLEANFILES = \
-	Debug_tags \
-	Trace_tags \
-	Debug_tags.tmp \
-	Trace_tags.tmp \
-	Debug_tags.h \
-	Trace_tags.h
-
-EXTRA_DIST = \
-	configuration.i \
-	exception.i \
-	mktagheaders \
-	mktags \
-	modal_exception.i
-
-%_tags.h: %_tags mktagheaders
-	$(AM_V_at)chmod +x @srcdir@/mktagheaders
-	$(AM_V_GEN)( @srcdir@/mktagheaders "$<" "$<" ) >"$@"
-
-# This .tmp business is to keep from having to re-compile options.cpp
-# (and then re-link the libraries) if nothing has changed.
-%_tags: %_tags.tmp
-	$(AM_V_GEN)\
-	diff -q "$^" "$@" &>/dev/null || mv "$^" "$@" || true
-# .PHONY ensures the .tmp version is always rebuilt (to check for any changes)
-.PHONY: Debug_tags.tmp Trace_tags.tmp
-# The "sed" invocation below is particularly obnoxious, but it works around
-# inconsistencies in REs on different platforms, using only a basic regular
-# expression (no |, no \<, ...).
-Debug_tags.tmp Trace_tags.tmp: mktags
-	$(AM_V_at)chmod +x @srcdir@/mktags
-	$(AM_V_GEN)(@srcdir@/mktags \
-    '$(@:_tags.tmp=)' \
-    "$$(find @srcdir@/../ -name '*.cpp' -o -name '*.h' -o -name '*.cc' -o -name '*.g')") >"$@"
diff --git a/src/bindings/Makefile b/src/bindings/Makefile
deleted file mode 100644
index 419d3a1b4..000000000
--- a/src/bindings/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/bindings
-
-include $(topdir)/Makefile.subdir
diff --git a/src/bindings/Makefile.am b/src/bindings/Makefile.am
deleted file mode 100644
index 9de484d1c..000000000
--- a/src/bindings/Makefile.am
+++ /dev/null
@@ -1,237 +0,0 @@
-# LIBCVC4BINDINGS_VERSION (-version-info) is in the form current:revision:age
-#
-# current -
-#   increment if interfaces have been added, removed or changed
-# revision -
-#   increment if source code has changed
-#   set to zero if current is incremented
-# age -
-#   increment if interfaces have been added
-#   set to zero if interfaces have been removed
-#   or changed
-#
-LIBCVC4BINDINGS_VERSION = @CVC4_BINDINGS_LIBRARY_VERSION@
-
-AUTOMAKE_OPTIONS = subdir-objects
-
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4BINDINGSLIB \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..
-AM_CXXFLAGS = -Wall
-
-# any binding-specific flags to pass to swig
-java_cpp_SWIGFLAGS = -package edu.nyu.acsys.CVC4
-
-lib_LTLIBRARIES =
-bin_PROGRAMS =
-javadatadir = $(datadir)/java
-javalibdir = $(libdir)/jni
-ocamldatadir = $(libdir)/ocaml/cvc4
-ocamllibdir = $(libdir)/ocaml/cvc4
-perldatadir = $(datadir)/perl5
-perllibdir = $(libdir)/perl5
-phpdatadir = $(datadir)/php
-phplibdir = $(libdir)/php
-pythondatadir = $(datadir)/pyshared
-pythonlibdir = $(libdir)/pyshared
-csharpdatadir = $(datadir)/csharp
-csharplibdir = $(libdir)/csharp
-rubylibdir = $(libdir)/ruby
-tcllibdir = $(libdir)/tcltk
-javadata_DATA =
-javalib_LTLIBRARIES=
-ocamldata_DATA =
-ocamllib_LTLIBRARIES=
-perldata_DATA =
-perllib_LTLIBRARIES =
-phpdata_DATA =
-phplib_LTLIBRARIES =
-pythondata_DATA =
-pythonlib_LTLIBRARIES =
-csharpdata_DATA =
-csharplib_LTLIBRARIES =
-rubylib_LTLIBRARIES =
-tcllib_LTLIBRARIES =
-if CVC4_HAS_SWIG
-if CVC4_LANGUAGE_BINDING_JAVA 
-javalib_LTLIBRARIES += java/libcvc4jni.la
-javadata_DATA += CVC4.jar
-java_libcvc4jni_la_LDFLAGS = \
-	-no-undefined \
-	-module \
-	-shrext $(CVC4_JAVA_MODULE_EXT) \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-java_libcvc4jni_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-endif
-if CVC4_LANGUAGE_BINDING_CSHARP
-csharplib_LTLIBRARIES += csharp/CVC4.la
-csharp_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-csharp_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-endif
-if CVC4_LANGUAGE_BINDING_PERL
-perllib_LTLIBRARIES += perl/CVC4.la
-perl_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-perl_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-perldata_DATA += perl/CVC4.pm
-endif
-if CVC4_LANGUAGE_BINDING_PHP
-phplib_LTLIBRARIES += php/CVC4.la
-php_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-php_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-phpdata_DATA += php/CVC4.php
-endif
-if CVC4_LANGUAGE_BINDING_PYTHON
-pythonlib_LTLIBRARIES += python/CVC4.la
-python_CVC4_la_CXXFLAGS = $(PYTHON_CXXFLAGS)
-python_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-python_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-pythondata_DATA += python/CVC4.py
-endif
-if CVC4_LANGUAGE_BINDING_OCAML
-ocamllib_LTLIBRARIES += ocaml/CVC4.la
-bin_PROGRAMS += cvc4_ocaml_top
-# We provide a make rule below, but we have to tell automake to lay off, too,
-# otherwise it tries (and fails) to package the nonexistent cvc4_ocaml_top.c!
-cvc4_ocaml_top_SOURCES =
-ocamldata_DATA += ocaml/swig.cmo ocaml/swig.cmi ocaml/swigp4.cmo ocaml/swigp4.cmi ocaml/CVC4.cmo ocaml/CVC4.cmi
-ocaml_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-ocaml_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-endif
-if CVC4_LANGUAGE_BINDING_RUBY
-rubylib_LTLIBRARIES += ruby/CVC4.la
-ruby_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-ruby_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-endif
-if CVC4_LANGUAGE_BINDING_TCL
-tcllib_LTLIBRARIES += tcl/CVC4.la
-tcl_CVC4_la_LDFLAGS = \
-	-module \
-	-version-info $(LIBCVC4BINDINGS_VERSION)
-tcl_CVC4_la_LIBADD = \
-	@builddir@/../libcvc4.la \
-	@builddir@/../parser/libcvc4parser.la
-endif
-# this endif matches the "if CVC4_HAS_SWIG" above
-endif
-
-nodist_java_libcvc4jni_la_SOURCES = java.cpp
-java_libcvc4jni_la_CXXFLAGS = -Wno-all @FNO_STRICT_ALIASING@ @WNO_UNUSED_VARIABLE@ @WNO_UNINITIALIZED@
-nodist_csharp_CVC4_la_SOURCES = csharp.cpp
-nodist_perl_CVC4_la_SOURCES = perl.cpp
-nodist_php_CVC4_la_SOURCES = php.cpp
-nodist_python_CVC4_la_SOURCES = python.cpp
-nodist_ocaml_CVC4_la_SOURCES = ocaml.cpp
-nodist_ruby_CVC4_la_SOURCES = ruby.cpp
-nodist_tcl_CVC4_la_SOURCES = tcl.cpp
-
-CLEANFILES = \
-	java.cpp \
-	csharp.cpp \
-	perl.cpp \
-	php.cpp \
-	python.cpp \
-	ocaml.cpp \
-	ruby.cpp \
-	tcl.cpp
-
-EXTRA_DIST = \
-	swig.h \
-	java_iterator_adapter.h \
-	java_stream_adapters.h
-
-MOSTLYCLEANFILES = \
-        .swig_deps \
-	$(patsubst %,%.d,$(filter-out c c++,$(CVC4_LANGUAGE_BINDINGS))) \
-	CVC4.jar
-
-java_libcvc4jni_la-java.lo: java.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(JAVA_CPPFLAGS) $(java_libcvc4jni_la_CXXFLAGS) -o $@ $<
-java.lo: java.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(JAVA_CPPFLAGS) $(java_libcvc4jni_la_CXXFLAGS) -o $@ $<
-CVC4.jar: java.cpp
-	$(AM_V_GEN) \
-	(cd java && \
-	rm -fr classes && \
-	mkdir -p classes && \
-	$(JAVAC) -source 1.6 -target 1.6 -classpath . -d classes `find . -name '*.java'` && \
-	cd classes) && \
-	$(JAR) cf $@ -C java/classes .
-#java.cpp:;
-csharp.lo: csharp.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(CSHARP_CPPFLAGS) -o $@ $<
-#csharp.cpp:;
-perl.lo: perl.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(PERL_CPPFLAGS) -o $@ $<
-#perl.cpp:;
-perl/CVC4.pm: perl.cpp
-php.lo: php.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(PHP_CPPFLAGS) -Iphp -o $@ $<
-#php.cpp:;
-python.lo: python.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(PYTHON_CPPFLAGS) -o $@ $<
-ocaml.lo: ocaml.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(OCAML_CPPFLAGS) -o $@ $<
-ocaml/swig.cmo: ocaml/swig.ml ocaml/swig.cmi; $(AM_V_GEN)$(OCAMLC) -I ocaml -c -o $@ $<
-ocaml/swig.cmi: ocaml/swig.mli; $(AM_V_GEN)$(OCAMLC) -I ocaml -c -o $@ $<
-ocaml/CVC4.cmo: ocaml/CVC4.ml ocaml/CVC4.cmi; $(AM_V_GEN)$(OCAMLC) -I ocaml -c -o $@ $<
-ocaml/CVC4.cmi: ocaml/CVC4.mli; $(AM_V_GEN)$(OCAMLC) -I ocaml -c -o $@ $<
-ocaml/swigp4.cmo: ocaml/swigp4.ml; $(AM_V_GEN)$(OCAMLFIND) ocamlc -package camlp4 -pp "$(CAMLP4O) pa_extend.cmo q_MLast.cmo" -o $@ -c $<
-ocaml/swig.ml:; $(AM_V_GEN)cd ocaml && $(SWIG) -ocaml -co swig.ml
-ocaml/swig.mli:; $(AM_V_GEN)cd ocaml && $(SWIG) -ocaml -co swig.mli
-ocaml/swigp4.ml:; $(AM_V_GEN)cd ocaml && $(SWIG) -ocaml -co swigp4.ml
-#ocaml.cpp:;
-cvc4_ocaml_top$(EXEEXT): ocaml/CVC4.la ocaml/swig.cmo ocaml/swig.cmi ocaml/swigp4.cmo ocaml/CVC4.cmo ocaml/CVC4.cmi
-	$(AM_V_GEN)\
-	$(OCAMLFIND) ocamlmktop -I $(ocamldatadir) -custom -o cvc4_ocaml_top$(EXEEXT) -package camlp4 dynlink.cma camlp4o.cma ocaml/swig.cmo ocaml/swigp4.cmo ocaml/CVC4.cmo -cclib ocaml/.libs/CVC4.so -cclib -lstdc++
-ruby.lo: ruby.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(RUBY_CPPFLAGS) -o $@ $<
-tcl.lo: tcl.cpp
-	$(AM_V_CXX)$(LTCXXCOMPILE) -c $(TCL_CPPFLAGS) -o $@ $<
-#tcl.cpp:;
-
-if CVC4_HAS_SWIG
-
-$(patsubst %,%.cpp,$(filter-out c c++,$(CVC4_LANGUAGE_BINDINGS))): %.cpp: @srcdir@/../cvc4.i
-	$(AM_V_at)mkdir -p $(patsubst %.cpp,%,$@)
-	$(AM_V_GEN)$(SWIG) -Wall -I@builddir@/.. -I@srcdir@/../include -I@srcdir@/.. -c++ -$(patsubst %.cpp,%,$@) -outdir $(patsubst %.cpp,%,$@) $($(subst .,_,$@)_SWIGFLAGS) -o $@ $<
-
-# Automake 1.16 is executing this target at configuration time. Because some
-# generated source files do not exist at that time, we use the -ignoremissing
-# option to not have SWIG complain about those missing files.
-$(patsubst %,%.d,$(filter-out c c++,$(CVC4_LANGUAGE_BINDINGS))): %.d: @srcdir@/../cvc4.i
-	$(AM_V_GEN)$(SWIG) -I@builddir@/.. -I@srcdir@/../include -I@srcdir@/.. -c++ -$(patsubst %.d,%,$@) -ignoremissing -MM -o $(patsubst %.d,%.cpp,$@) $<
-# .PHONY so they get rebuilt each time
-.PHONY: .swig_deps $(patsubst %,%.d,$(filter-out c c++,$(CVC4_LANGUAGE_BINDINGS)))
-.swig_deps: $(patsubst %,%.d,$(filter-out c c++,$(CVC4_LANGUAGE_BINDINGS)))
-	$(AM_V_GEN)cat $+ </dev/null >$@
-@mk_include@ .swig_deps
-
-endif
-
-clean-local:; rm -fr $(patsubst %.cpp,%,$(filter-out c c++,$(CVC4_LANGUAGE_BINDINGS)))
diff --git a/src/expr/.gitignore b/src/expr/.gitignore
deleted file mode 100644
index 238db3ad3..000000000
--- a/src/expr/.gitignore
+++ /dev/null
@@ -1,6 +0,0 @@
-/kind.h
-/metakind.h
-/expr.cpp
-/expr.h
-/expr_manager.cpp
-/expr_manager.h
diff --git a/src/expr/Makefile b/src/expr/Makefile
deleted file mode 100644
index eff3b332e..000000000
--- a/src/expr/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/expr
-
-include $(topdir)/Makefile.subdir
diff --git a/src/expr/Makefile.am b/src/expr/Makefile.am
deleted file mode 100644
index f8f9dbd11..000000000
--- a/src/expr/Makefile.am
+++ /dev/null
@@ -1,228 +0,0 @@
-# if coverage is enabled:
-# COVERAGE_ON = yes from configure.ac
-# Using an inline conditional function to choose between absolute and
-# relative paths for options files
-# lcov does not support relative paths and src/options and src/expr
-# in particular were breaking it
-# Building with coverage will cause portability issues in some cases
-
-VPATH = $(if $(COVERAGE_ON), $(realpath @srcdir@), @srcdir@)
-
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	$(if $(COVERAGE_ON), -I@abs_builddir@/.. -I@abs_srcdir@/../include -I@abs_srcdir@/.., \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..)
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = libexpr.la
-
-# For some reason statistics were in libutil. No idea why though.
-libexpr_la_SOURCES = \
-	array.h \
-	array_store_all.cpp \
-	array_store_all.h \
-	ascription_type.h \
-	attribute.h \
-	attribute.cpp \
-	attribute_internals.h \
-	attribute_unique_id.h \
-	chain.h \
-	emptyset.cpp \
-	emptyset.h \
-	expr_iomanip.cpp \
-	expr_iomanip.h \
-	expr_manager_scope.h \
-	expr_stream.h \
-	kind_map.h \
-	matcher.h \
-	node.cpp \
-	node.h \
-	node_algorithm.cpp \
-	node_algorithm.h \
-	node_builder.h \
-	node_manager.cpp \
-	node_manager.h \
-	node_manager_attributes.h \
-	node_manager_listeners.cpp \
-	node_manager_listeners.h \
-	node_self_iterator.h \
-	node_value.cpp \
-	node_value.h \
-	pickle_data.cpp \
-	pickle_data.h \
-	pickler.cpp \
-	pickler.h \
-	symbol_table.cpp \
-	symbol_table.h \
-	type.cpp \
-	type.h \
-	type_checker.h \
-	type_node.cpp \
-	type_node.h \
-	variable_type_map.h \
-	datatype.h \
-	datatype.cpp \
-	record.cpp \
-	record.h \
-	uninterpreted_constant.cpp \
-	uninterpreted_constant.h
-
-nodist_libexpr_la_SOURCES = \
-	kind.h \
-	kind.cpp \
-	metakind.h \
-	metakind.cpp \
-	type_properties.h \
-	expr.h \
-	expr.cpp \
-	expr_manager.h \
-	expr_manager.cpp \
-	type_checker.cpp
-
-EXTRA_DIST = \
-	array.i \
-	chain.i \
-	array_store_all.i \
-	ascription_type.i \
-	datatype.i \
-	emptyset.i \
-	kind_template.h \
-	kind_template.cpp \
-	metakind_template.h \
-	metakind_template.cpp \
-	type_properties_template.h \
-	expr_manager_template.h \
-	expr_manager_template.cpp \
-	expr_template.h \
-	expr_template.cpp \
-	type_checker_template.cpp \
-	mkkind \
-	mkmetakind \
-	mkexpr \
-	expr_stream.i \
-	expr_manager.i \
-	symbol_table.i \
-	type.i \
-	kind.i \
-	expr.i \
-	record.i \
-	variable_type_map.i \
-	uninterpreted_constant.i
-
-BUILT_SOURCES = \
-	kind.h \
-	kind.cpp \
-	metakind.h \
-	metakind.cpp \
-	type_properties.h \
-	expr.h \
-	expr.cpp \
-	expr_manager.h \
-	expr_manager.cpp \
-	type_checker.cpp \
-	$(top_builddir)/src/expr/.subdirs
-
-CLEANFILES = \
-	kind.h \
-	kind.cpp \
-	metakind.h \
-	metakind.cpp \
-	expr.h \
-	expr.cpp \
-	expr_manager.h \
-	expr_manager.cpp \
-	type_checker.cpp \
-	type_properties.h \
-	$(top_builddir)/src/expr/.subdirs
-
-$(top_builddir)/src/expr/.subdirs: $(top_srcdir)/src/Makefile.theories  @top_srcdir@/src/mksubdirs
-	$(AM_V_at)test -d $(top_builddir)/src/expr || mkdir $(top_builddir)/src/expr
-	$(AM_V_at)chmod +x @top_srcdir@/src/mksubdirs
-	$(AM_V_at)( @top_srcdir@/src/mksubdirs $(if $(COVERAGE_ON), "$(abs_top_srcdir)", "$(top_srcdir)")) > $(top_builddir)/src/expr/.subdirs.tmp
-	@if ! diff -q $(top_builddir)/src/expr/.subdirs $(top_builddir)/src/expr/.subdirs.tmp &>/dev/null; then \
-		echo "  GEN   " $@; \
-		$(am__mv) $(top_builddir)/src/expr/.subdirs.tmp $(top_builddir)/src/expr/.subdirs; \
-	fi
-
-kind.h: kind_template.h mkkind @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkkind
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkkind \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-kind.cpp: kind_template.cpp mkkind @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkkind
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkkind \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-metakind.h: metakind_template.h mkmetakind @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkmetakind
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkmetakind \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-metakind.cpp: metakind_template.cpp mkmetakind @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkmetakind
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkmetakind \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-type_properties.h: type_properties_template.h mkkind @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkkind
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkkind \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-expr.h: expr_template.h mkexpr @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkexpr
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkexpr \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-expr.cpp: expr_template.cpp mkexpr @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkexpr
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkexpr \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-expr_manager.h: expr_manager_template.h mkexpr @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkexpr
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkexpr \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-expr_manager.cpp: expr_manager_template.cpp mkexpr @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkexpr
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkexpr \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-type_checker.cpp: type_checker_template.cpp mkexpr @top_builddir@/src/expr/.subdirs $(if $(COVERAGE_ON), @abs_top_srcdir@, @top_srcdir@)/src/theory/*/kinds
-	$(AM_V_at)chmod +x @srcdir@/mkexpr
-	$(AM_V_at)$(am__mv) $@ $@~ 2>/dev/null || true
-	$(AM_V_GEN)(@srcdir@/mkexpr \
-		$< \
-		`cat @top_builddir@/src/expr/.subdirs` \
-	> $@) || (rm -f $@ && exit 1)
-
-.PHONY: builts
-builts: $(BUILT_SOURCES)
diff --git a/src/include/.gitignore b/src/include/.gitignore
deleted file mode 100644
index 274bc504a..000000000
--- a/src/include/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-/Makefile
-
diff --git a/src/lib/Makefile b/src/lib/Makefile
deleted file mode 100644
index 9811fec4f..000000000
--- a/src/lib/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/lib
-
-include $(topdir)/Makefile.subdir
diff --git a/src/lib/Makefile.am b/src/lib/Makefile.am
deleted file mode 100644
index aec9fa634..000000000
--- a/src/lib/Makefile.am
+++ /dev/null
@@ -1,25 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..
-AM_CFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-# This is a workaround for now to fix some warnings related to unsupported
-# compiler flags since we are compiling C code here. CXXFLAGS is set via
-# configure, however, we should actually set AM_CXXFLAGS.
-CXXFLAGS = $(AM_CXXFLAGS)
-
-noinst_LTLIBRARIES = libreplacements.la
-
-libreplacements_la_SOURCES =
-
-libreplacements_la_LIBADD = \
-	$(LTLIBOBJS)
-
-EXTRA_DIST = \
-	replacements.h \
-	clock_gettime.c \
-	clock_gettime.h \
-	strtok_r.c \
-	strtok_r.h \
-	ffs.c \
-	ffs.h
diff --git a/src/main/Makefile b/src/main/Makefile
deleted file mode 100644
index 5e936ee06..000000000
--- a/src/main/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/main
-
-include $(topdir)/Makefile.subdir
diff --git a/src/main/Makefile.am b/src/main/Makefile.am
deleted file mode 100644
index 372e817f6..000000000
--- a/src/main/Makefile.am
+++ /dev/null
@@ -1,85 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4DRIVER \
-	-I@builddir@/.. $(ANTLR_INCLUDES) -I@srcdir@/../include -I@srcdir@/..
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas
-
-bin_PROGRAMS = cvc4
-
-noinst_LIBRARIES = libmain.a
-
-libmain_a_SOURCES = \
-	interactive_shell.h \
-	interactive_shell.cpp \
-	main.h \
-	util.cpp
-
-if CVC4_BUILD_PCVC4
-bin_PROGRAMS += pcvc4
-pcvc4_SOURCES = \
-	main.cpp \
-	portfolio.cpp \
-	portfolio.h \
-	portfolio_util.cpp \
-	portfolio_util.h \
-	command_executor.cpp \
-	command_executor_portfolio.cpp \
-	command_executor.h \
-	command_executor_portfolio.h \
-	driver_unified.cpp
-pcvc4_LDADD = \
-	libmain.a \
-	@builddir@/../parser/libcvc4parser.la \
-	@builddir@/../libcvc4.la \
-	$(READLINE_LIBS) \
-	@builddir@/../lib/libreplacements.la
-
-pcvc4_CPPFLAGS = $(AM_CPPFLAGS) $(BOOST_CPPFLAGS) -DPORTFOLIO_BUILD
-pcvc4_LDADD += $(BOOST_THREAD_LIBS)
-pcvc4_LDADD += $(BOOST_THREAD_LDFLAGS)
-
-if STATIC_BINARY
-pcvc4_LINK = $(CXXLINK) -all-static $(pcvc4_LDFLAGS)
-else
-pcvc4_LINK = $(CXXLINK) $(pcvc4_LDFLAGS)
-endif
-endif
-
-cvc4_SOURCES = \
-	main.cpp \
-	command_executor.cpp \
-	driver_unified.cpp
-cvc4_LDADD = \
-	libmain.a \
-	@builddir@/../parser/libcvc4parser.la \
-	@builddir@/../libcvc4.la \
-	$(READLINE_LIBS) \
-	@builddir@/../lib/libreplacements.la
-
-BUILT_SOURCES = \
-	$(TOKENS_FILES)
-
-TOKENS_FILES = \
-	cvc_tokens.h \
-	smt1_tokens.h \
-	smt2_tokens.h \
-	tptp_tokens.h
-
-cvc_tokens.h: @srcdir@/../parser/cvc/Cvc.g
-	$(AM_V_GEN)grep "'[a-zA-Z][a-zA-Z0-9_-][a-zA-Z0-9_-]*'" $^ | sed 's/.*'\''\([a-zA-Z0-9_-]*\)'\''.*/"\1",/' | sort -u >$@
-smt1_tokens.h: @srcdir@/../parser/smt1/Smt1.g
-	$(AM_V_GEN)grep "'[a-zA-Z][a-zA-Z0-9_-][a-zA-Z0-9_-]*'" $^ | sed 's/.*'\''\([a-zA-Z0-9_-]*\)'\''.*/"\1",/' | sort -u >$@
-smt2_tokens.h: @srcdir@/../parser/smt2/Smt2.g
-	$(AM_V_GEN)grep "'[a-zA-Z][a-zA-Z0-9_-][a-zA-Z0-9_-]*'" $^ | sed 's/.*'\''\([a-zA-Z0-9_-]*\)'\''.*/"\1",/' | sort -u >$@
-tptp_tokens.h: @srcdir@/../parser/tptp/Tptp.g
-	$(AM_V_GEN)grep "'[a-zA-Z][a-zA-Z0-9_-][a-zA-Z0-9_-]*'" $^ | sed 's/.*'\''\([a-zA-Z0-9_-]*\)'\''.*/"\1",/' | sort -u >$@
-
-
-clean-local:
-	rm -f $(BUILT_SOURCES)
-
-if STATIC_BINARY
-cvc4_LINK = $(CXXLINK) -all-static $(cvc4_LDFLAGS)
-else
-cvc4_LINK = $(CXXLINK) $(cvc4_LDFLAGS)
-endif
-
diff --git a/src/mksubdirs b/src/mksubdirs
deleted file mode 100755
index c96437caa..000000000
--- a/src/mksubdirs
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-#
-# The purpose of this file is to generate a .subdirs file in the build process.
-# This file contains a file of relative paths to all of the theories relative
-# to the current directory. Each Makefile.am should thus build its own .subdirs file.
-# This assumes it is passed the equivalent of the $top_srcdir configure variable.
-#
-# Invocation:
-#
-#    mksubdirs <top_srcdir>
-
-TOP_SRCDIR=$1
-
-grep '^THEORIES = ' $TOP_SRCDIR/src/Makefile.theories | \
-  cut -d' ' -f3- | tr ' ' "\n" | \
-  xargs -I__D__ echo "$TOP_SRCDIR/src/theory/__D__/kinds"
diff --git a/src/options/Makefile b/src/options/Makefile
deleted file mode 100644
index 54a46191d..000000000
--- a/src/options/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/options
-
-include $(topdir)/Makefile.subdir
diff --git a/src/options/Makefile.am b/src/options/Makefile.am
deleted file mode 100644
index 498989c80..000000000
--- a/src/options/Makefile.am
+++ /dev/null
@@ -1,159 +0,0 @@
-# if coverage is enabled:
-# COVERAGE_ON = yes from configure.ac
-# Using an inline conditional function to choose between absolute and
-# relative paths for options files
-# lcov does not support relative paths and src/options and src/expr
-# in particular were breaking it
-# Building with coverage will cause portability issues in some cases
-
-VPATH = $(if $(COVERAGE_ON), $(realpath @srcdir@), @srcdir@)
-
-OPTIONS_CONFIG_FILES = \
-	arith_options.toml \
-	arrays_options.toml \
-	base_options.toml \
-	booleans_options.toml \
-	builtin_options.toml \
-	bv_options.toml \
-	datatypes_options.toml \
-	decision_options.toml \
-	expr_options.toml \
-	fp_options.toml \
-	idl_options.toml \
-	main_options.toml \
-	parser_options.toml \
-	printer_options.toml \
-	proof_options.toml \
-	prop_options.toml \
-	quantifiers_options.toml \
-	sep_options.toml \
-	sets_options.toml \
-	smt_options.toml \
-	strings_options.toml \
-	theory_options.toml \
-	uf_options.toml
-
-OPTIONS_GEN_H = $(OPTIONS_CONFIG_FILES:.toml=.h)
-
-OPTIONS_GEN_CPP = $(OPTIONS_CONFIG_FILES:.toml=.cpp)
-
-CPP_TEMPLATE_FILES = \
-	module_template.h \
-	module_template.cpp \
-	options_holder_template.h \
-	options_template.cpp
-
-DOCUMENTATION_FILES = \
-	../../doc/cvc4.1 \
-	../../doc/SmtEngine.3cvc \
-	../../doc/options.3cvc
-
-DOCUMENTATION_TEMPLATE_FILES = \
-	../../doc/cvc4.1_template \
-	../../doc/SmtEngine.3cvc_template \
-	../../doc/options.3cvc_template
-
-
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	$(if $(COVERAGE_ON), -I@abs_builddir@/.. -I@abs_srcdir@/../include -I@abs_srcdir@/.., \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..)
-AM_CXXFLAGS = -Wall $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = liboptions.la
-
-liboptions_la_SOURCES = \
-	arith_heuristic_pivot_rule.cpp \
-	arith_heuristic_pivot_rule.h \
-	arith_propagation_mode.cpp \
-	arith_propagation_mode.h \
-	arith_unate_lemma_mode.cpp \
-	arith_unate_lemma_mode.h \
-	argument_extender_implementation.cpp \
-	argument_extender_implementation.h \
-	argument_extender.h \
-	base_handlers.h \
-	bv_bitblast_mode.cpp \
-	bv_bitblast_mode.h \
-	datatypes_modes.h \
-	decision_mode.cpp \
-	decision_mode.h \
-	decision_weight.h \
-	didyoumean.cpp \
-	didyoumean.h \
-	language.cpp \
-	language.h \
-	open_ostream.cpp \
-	open_ostream.h \
-	option_exception.cpp \
-	option_exception.h \
-	options.h \
-	options_handler.cpp \
-	options_handler.h \
-	options_public_functions.cpp \
-	printer_modes.cpp \
-	printer_modes.h \
-	quantifiers_modes.cpp \
-	quantifiers_modes.h \
-	set_language.cpp \
-	set_language.h \
-	smt_modes.cpp \
-	smt_modes.h \
-	sygus_out_mode.h \
-	theoryof_mode.cpp \
-	theoryof_mode.h \
-	ufss_mode.h
-
-
-nodist_liboptions_la_SOURCES = \
-	options.cpp \
-	options_holder.h \
-	$(OPTIONS_GEN_H) \
-	$(OPTIONS_GEN_CPP)
-
-
-BUILT_SOURCES = \
-	options.cpp
-
-
-CLEANFILES = \
-	$(BUILT_SOURCES) \
-	$(OPTIONS_GEN_H) \
-	$(OPTIONS_GEN_CPP) \
-	$(DOCUMENTATION_FILES) \
-	options_holder.h
-
-
-EXTRA_DIST = \
-	options.cpp \
-	options_holder.h \
-	$(OPTIONS_GEN_CPP) \
-	$(OPTIONS_GEN_H) \
-	$(OPTIONS_CONFIG_FILES) \
-	$(CPP_TEMPLATE_FILES) \
-	$(DOCUMENTATION_FILES) \
-	mkoptions.py \
-	language.i \
-	option_exception.i \
-	options.i
-
-
-
-# Make sure the implicit rules never mistake a _template.cpp or _template.h
-# file for source file.
-$(CPP_TEMPLATE_FILES):;
-
-# All source/doc files are generated in one pass with rule options.cpp. Note
-# that this is done incrementally since mkoptions.py checks if a generated file
-# changed before writing to the file. No global re-compilation of all generated
-# files happens if only individual files were modified.
-$(OPTIONS_GEN_CPP) $(OPTIONS_GEN_H) options_holder.h $(DOCUMENTATION_FILES): options.cpp
-
-options.cpp: mkoptions.py $(CPP_TEMPLATE_FILES) $(OPTIONS_CONFIG_FILES) $(DOCUMENTATION_TEMPLATE_FILES)
-	$(PYTHON) @srcdir@/mkoptions.py @abs_srcdir@ ../../doc . $(addprefix @abs_srcdir@/, $(OPTIONS_CONFIG_FILES))
-
-# This rule is ugly.  It's needed to ensure that automake's dependence
-# includes are available during distclean, even though they come from
-# directories that are cleaned first.  Without this rule, "distclean"
-# fails.
-%.Plo:; $(MKDIR_P) "$(dir $@)" && : > "$@"
diff --git a/src/parser/Makefile b/src/parser/Makefile
deleted file mode 100644
index cef81750e..000000000
--- a/src/parser/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/parser
-
-include $(topdir)/Makefile.subdir
diff --git a/src/parser/Makefile.am b/src/parser/Makefile.am
deleted file mode 100644
index 98b98ccaf..000000000
--- a/src/parser/Makefile.am
+++ /dev/null
@@ -1,76 +0,0 @@
-# LIBCVC4PARSER_VERSION (-version-info) is in the form current:revision:age
-#
-# current -
-#   increment if interfaces have been added, removed or changed
-# revision -
-#   increment if source code has changed
-#   set to zero if current is incremented
-# age -
-#   increment if interfaces have been added
-#   set to zero if interfaces have been removed
-#   or changed
-#
-LIBCVC4PARSER_VERSION = @CVC4_PARSER_LIBRARY_VERSION@
-
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4PARSERLIB \
-	-I@builddir@/.. $(ANTLR_INCLUDES) -I@srcdir@/../include -I@srcdir@/..
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-SUBDIRS = smt1 smt2 cvc tptp
-
-lib_LTLIBRARIES = libcvc4parser.la
-
-libcvc4parser_la_LDFLAGS = \
-	$(ANTLR_LDFLAGS) \
-	-no-undefined \
-	-version-info $(LIBCVC4PARSER_VERSION)
-
-if CVC4_WINDOWS_BUILD
-# -Wl,--export-all-symbols makes sure that all symbols are exported when
-# building a DLL. This option is on by default but gets disabled for the parser
-# library because the generated lexer/parser files define some functions as
-# __declspec(dllexport), which leads to lots of unresolved symbols when linking
-# against libcvc4parser.
-libcvc4parser_la_LDFLAGS += -Wl,--export-all-symbols
-endif
-
-libcvc4parser_la_LIBADD = \
-	@builddir@/smt1/libparsersmt1.la \
-	@builddir@/smt2/libparsersmt2.la \
-	@builddir@/tptp/libparsertptp.la \
-	@builddir@/cvc/libparsercvc.la \
-	@builddir@/../libcvc4.la \
-	@builddir@/../lib/libreplacements.la
-
-libcvc4parser_la_SOURCES = \
-	antlr_input.cpp \
-	antlr_input.h \
-	antlr_input_imports.cpp \
-	antlr_line_buffered_input.cpp \
-	antlr_line_buffered_input.h \
-	antlr_tracing.h \
-	antlr_undefines.h \
-	bounded_token_buffer.cpp \
-	bounded_token_buffer.h \
-	bounded_token_factory.cpp \
-	bounded_token_factory.h \
-	input.cpp \
-	input.h \
-	line_buffer.cpp \
-	line_buffer.h \
-	memory_mapped_input_buffer.cpp \
-	memory_mapped_input_buffer.h \
-	parser.cpp \
-	parser.h \
-	parser_builder.cpp \
-	parser_builder.h \
-	parser_exception.h
-
-EXTRA_DIST = \
-	Makefile.antlr_tracing \
-	cvc4parser.i \
-	input.i \
-	parser_builder.i \
-	parser_exception.i \
-	parser.i
diff --git a/src/parser/Makefile.antlr_tracing b/src/parser/Makefile.antlr_tracing
deleted file mode 100644
index fa79337b4..000000000
--- a/src/parser/Makefile.antlr_tracing
+++ /dev/null
@@ -1,22 +0,0 @@
-# -*-makefile-*-
-#
-# This makefile is included from parser directories in order to
-# do antlr tracing.  THIS IS VERY MUCH A HACK, and is only enabled
-# if CVC4_TRACE_ANTLR is defined (and not 0).  In ANTLR 3.2, we
-# have to #define "println" and "System," etc., because the
-# generator erroneously puts Java in C output!
-#
-
-ifeq ($(CVC4_TRACE_ANTLR),)
-else
-
-ifeq ($(CVC4_TRACE_ANTLR),0)
-else
-
-AM_CPPFLAGS += -DCVC4_TRACE_ANTLR
-ANTLR_OPTS += -trace
-
-endif
-
-endif
-
diff --git a/src/parser/cvc/Makefile b/src/parser/cvc/Makefile
deleted file mode 100644
index cbcc0a493..000000000
--- a/src/parser/cvc/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../../..
-srcdir = src/parser/cvc
-
-include $(topdir)/Makefile.subdir
diff --git a/src/parser/cvc/Makefile.am b/src/parser/cvc/Makefile.am
deleted file mode 100644
index ff3308d89..000000000
--- a/src/parser/cvc/Makefile.am
+++ /dev/null
@@ -1,68 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4PARSERLIB \
-	-I@builddir@/../.. -I@srcdir@/../../include -I@srcdir@/../.. $(ANTLR_INCLUDES)
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN) $(WNO_PARENTHESES) $(WNO_TAUTOLOGICAL_COMPARE) -Wno-unused-function -Wno-unused-variable $(WNO_UNINITIALIZED) $(WNO_CONVERSION_NULL)
-
-# Compile generated C files using C++ compiler
-AM_CFLAGS = $(AM_CXXFLAGS)
-CFLAGS=$(CXXFLAGS)
-CC=$(CXX)
-
-ANTLR_OPTS =
-
-# hide this included makefile from automake
-@mk_include@ @srcdir@/../Makefile.antlr_tracing
-
-noinst_LTLIBRARIES = libparsercvc.la
-
-ANTLR_TOKEN_STUFF = \
-	@builddir@/Cvc.tokens
-ANTLR_LEXER_STUFF = \
-	@builddir@/CvcLexer.h \
-	@builddir@/CvcLexer.c \
-	$(ANTLR_TOKEN_STUFF)
-ANTLR_PARSER_STUFF = \
-	@builddir@/CvcParser.h \
-	@builddir@/CvcParser.c
-ANTLR_STUFF = \
-	$(ANTLR_LEXER_STUFF) \
-	$(ANTLR_PARSER_STUFF)
-
-libparsercvc_la_SOURCES = \
-	Cvc.g \
-	cvc_input.h \
-	cvc_input.cpp \
-	$(ANTLR_STUFF)
-
-BUILT_SOURCES = \
-	@builddir@/Cvc.tokens \
-	@builddir@/CvcLexer.h \
-	@builddir@/CvcLexer.c \
-	@builddir@/CvcParser.h \
-	@builddir@/CvcParser.c \
-	stamp-generated
-
-EXTRA_DIST = \
-	README \
-	stamp-generated
-
-DISTCLEANFILES = $(ANTLR_STUFF)
-distclean-local:
-	-$(AM_V_at)rmdir generated
-	-$(AM_V_at)rm -f stamp-generated
-
-stamp-generated:
-	$(AM_V_at)mkdir -p generated
-	$(AM_V_at)touch stamp-generated
-
-# antlr doesn't overwrite output files, it just leaves them.  So we have to delete them first.
-@builddir@/CvcLexer.h: Cvc.g stamp-generated
-	-$(AM_V_at)rm -f $(ANTLR_STUFF)
-	@if test -z "$(ANTLR)"; then echo "ERROR: antlr parser generator cannot be found, cannot generate the parser" >&2; exit 1; fi
-	$(AM_V_GEN)$(ANTLR) $(ANTLR_OPTS) -fo "@builddir@" "@srcdir@/Cvc.g"
-
-# These don't actually depend on CvcLexer.h, but if we're doing parallel
-# make and the lexer needs to be rebuilt, we have to keep the rules
-# from running in parallel (since the token files will be deleted &
-# recreated)
-@builddir@/CvcLexer.c @builddir@/CvcParser.h @builddir@/CvcParser.c $(ANTLR_TOKEN_STUFF): @builddir@/CvcLexer.h
diff --git a/src/parser/smt1/Makefile b/src/parser/smt1/Makefile
deleted file mode 100644
index 7e97ed357..000000000
--- a/src/parser/smt1/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../../..
-srcdir = src/parser/smt
-
-include $(topdir)/Makefile.subdir
diff --git a/src/parser/smt1/Makefile.am b/src/parser/smt1/Makefile.am
deleted file mode 100644
index f5320002d..000000000
--- a/src/parser/smt1/Makefile.am
+++ /dev/null
@@ -1,69 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4PARSERLIB \
-	-I@builddir@/../.. -I@srcdir@/../../include -I@srcdir@/../.. $(ANTLR_INCLUDES)
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN) $(WNO_PARENTHESES) $(WNO_TAUTOLOGICAL_COMPARE) -Wno-unused-function -Wno-unused-variable
-
-# Compile generated C files using C++ compiler
-AM_CFLAGS = $(AM_CXXFLAGS)
-CFLAGS=$(CXXFLAGS)
-CC=$(CXX)
-
-ANTLR_OPTS =
-
-# hide this included makefile from automake
-@mk_include@ @srcdir@/../Makefile.antlr_tracing
-
-noinst_LTLIBRARIES = libparsersmt1.la
-
-ANTLR_TOKEN_STUFF = \
-	@builddir@/Smt1.tokens
-ANTLR_LEXER_STUFF = \
-	@builddir@/Smt1Lexer.h \
-	@builddir@/Smt1Lexer.c \
-	$(ANTLR_TOKEN_STUFF)
-ANTLR_PARSER_STUFF = \
-	@builddir@/Smt1Parser.h \
-	@builddir@/Smt1Parser.c
-ANTLR_STUFF = \
-	$(ANTLR_LEXER_STUFF) \
-	$(ANTLR_PARSER_STUFF)
-
-libparsersmt1_la_SOURCES = \
-	Smt1.g \
-        smt1.h \
-        smt1.cpp \
-	smt1_input.h \
-	smt1_input.cpp \
-	$(ANTLR_STUFF)
-
-BUILT_SOURCES = \
-	@builddir@/Smt1.tokens \
-	@builddir@/Smt1Lexer.h \
-	@builddir@/Smt1Lexer.c \
-	@builddir@/Smt1Parser.h \
-	@builddir@/Smt1Parser.c \
-	stamp-generated
-
-EXTRA_DIST = \
-	stamp-generated
-
-DISTCLEANFILES = $(ANTLR_STUFF)
-distclean-local:
-	-$(AM_V_at)rmdir generated
-	-$(AM_V_at)rm -f stamp-generated
-
-stamp-generated:
-	$(AM_V_at)mkdir -p generated
-	$(AM_V_at)touch stamp-generated
-
-# antlr doesn't overwrite output files, it just leaves them.  So we have to delete them first.
-@builddir@/Smt1Lexer.h: Smt1.g stamp-generated
-	-$(AM_V_at)rm -f $(ANTLR_STUFF)
-	@if test -z "$(ANTLR)"; then echo "ERROR: antlr parser generator cannot be found, cannot generate the parser" >&2; exit 1; fi
-	$(AM_V_GEN)$(ANTLR) $(ANTLR_OPTS) -fo "@builddir@" "@srcdir@/Smt1.g"
-
-# These don't actually depend on Smt1Lexer.h, but if we're doing parallel
-# make and the lexer needs to be rebuilt, we have to keep the rules
-# from running in parallel (since the token files will be deleted &
-# recreated)
-@builddir@/Smt1Lexer.c @builddir@/Smt1Parser.h @builddir@/Smt1Parser.c $(ANTLR_TOKEN_STUFF): @builddir@/Smt1Lexer.h
diff --git a/src/parser/smt2/Makefile b/src/parser/smt2/Makefile
deleted file mode 100644
index fc9cc6db2..000000000
--- a/src/parser/smt2/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../../..
-srcdir = src/parser/smt2
-
-include $(topdir)/Makefile.subdir
diff --git a/src/parser/smt2/Makefile.am b/src/parser/smt2/Makefile.am
deleted file mode 100644
index 995e442e6..000000000
--- a/src/parser/smt2/Makefile.am
+++ /dev/null
@@ -1,71 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4PARSERLIB \
-	-I@builddir@/../.. -I@srcdir@/../../include -I@srcdir@/../.. $(ANTLR_INCLUDES)
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN) $(WNO_PARENTHESES) $(WNO_TAUTOLOGICAL_COMPARE) -Wno-unused-function -Wno-unused-variable
-
-# Compile generated C files using C++ compiler
-AM_CFLAGS = $(AM_CXXFLAGS)
-CFLAGS=$(CXXFLAGS)
-CC=$(CXX)
-
-ANTLR_OPTS =
-
-# hide this included makefile from automake
-@mk_include@ @srcdir@/../Makefile.antlr_tracing
-
-noinst_LTLIBRARIES = libparsersmt2.la
-
-ANTLR_TOKEN_STUFF = \
-	@builddir@/Smt2.tokens
-ANTLR_LEXER_STUFF = \
-	@builddir@/Smt2Lexer.h \
-	@builddir@/Smt2Lexer.c \
-	$(ANTLR_TOKEN_STUFF)
-ANTLR_PARSER_STUFF = \
-	@builddir@/Smt2Parser.h \
-	@builddir@/Smt2Parser.c
-ANTLR_STUFF = \
-	$(ANTLR_LEXER_STUFF) \
-	$(ANTLR_PARSER_STUFF)
-
-libparsersmt2_la_SOURCES = \
-	Smt2.g \
-	smt2.h \
-	smt2.cpp \
-	smt2_input.h \
-	smt2_input.cpp \
-	sygus_input.h \
-	sygus_input.cpp \
-	$(ANTLR_STUFF)
-
-BUILT_SOURCES = \
-	@builddir@/Smt2.tokens \
-	@builddir@/Smt2Lexer.h \
-	@builddir@/Smt2Lexer.c \
-	@builddir@/Smt2Parser.h \
-	@builddir@/Smt2Parser.c \
-	stamp-generated
-
-EXTRA_DIST = \
-	stamp-generated
-
-DISTCLEANFILES = $(ANTLR_STUFF)
-distclean-local:
-	-$(AM_V_at)rmdir generated
-	-$(AM_V_at)rm -f stamp-generated
-
-stamp-generated:
-	$(AM_V_at)mkdir -p generated
-	$(AM_V_at)touch stamp-generated
-
-# antlr doesn't overwrite output files, it just leaves them.  So we have to delete them first.
-@builddir@/Smt2Lexer.h: Smt2.g stamp-generated
-	-$(AM_V_at)rm -f $(ANTLR_STUFF)
-	@if test -z "$(ANTLR)"; then echo "ERROR: antlr parser generator cannot be found, cannot generate the parser" >&2; exit 1; fi
-	$(AM_V_GEN)$(ANTLR) $(ANTLR_OPTS) -fo "@builddir@" "@srcdir@/Smt2.g"
-
-# These don't actually depend on SmtLexer.h, but if we're doing parallel
-# make and the lexer needs to be rebuilt, we have to keep the rules
-# from running in parallel (since the token files will be deleted &
-# recreated)
-@builddir@/Smt2Lexer.c @builddir@/Smt2Parser.h @builddir@/Smt2Parser.c $(ANTLR_TOKEN_STUFF): @builddir@/Smt2Lexer.h
diff --git a/src/parser/tptp/Makefile b/src/parser/tptp/Makefile
deleted file mode 100644
index 45cde5821..000000000
--- a/src/parser/tptp/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../../..
-srcdir = src/parser/tptp
-
-include $(topdir)/Makefile.subdir
diff --git a/src/parser/tptp/Makefile.am b/src/parser/tptp/Makefile.am
deleted file mode 100644
index 43bbc595d..000000000
--- a/src/parser/tptp/Makefile.am
+++ /dev/null
@@ -1,69 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4PARSERLIB \
-	-I@builddir@/../.. -I@srcdir@/../../include -I@srcdir@/../.. $(ANTLR_INCLUDES)
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN) $(WNO_PARENTHESES) $(WNO_TAUTOLOGICAL_COMPARE) -Wno-unused-function -Wno-unused-variable
-
-# Compile generated C files using C++ compiler
-AM_CFLAGS = $(AM_CXXFLAGS)
-CFLAGS=$(CXXFLAGS)
-CC=$(CXX)
-
-ANTLR_OPTS =
-
-# hide this included makefile from automake
-@mk_include@ @srcdir@/../Makefile.antlr_tracing
-
-noinst_LTLIBRARIES = libparsertptp.la
-
-ANTLR_TOKEN_STUFF = \
-	@builddir@/Tptp.tokens
-ANTLR_LEXER_STUFF = \
-	@builddir@/TptpLexer.h \
-	@builddir@/TptpLexer.c \
-	$(ANTLR_TOKEN_STUFF)
-ANTLR_PARSER_STUFF = \
-	@builddir@/TptpParser.h \
-	@builddir@/TptpParser.c
-ANTLR_STUFF = \
-	$(ANTLR_LEXER_STUFF) \
-	$(ANTLR_PARSER_STUFF)
-
-libparsertptp_la_SOURCES = \
-	Tptp.g \
-	tptp.h \
-	tptp.cpp \
-	tptp_input.h \
-	tptp_input.cpp \
-	$(ANTLR_STUFF)
-
-BUILT_SOURCES = \
-	@builddir@/Tptp.tokens \
-	@builddir@/TptpLexer.h \
-	@builddir@/TptpLexer.c \
-	@builddir@/TptpParser.h \
-	@builddir@/TptpParser.c \
-	stamp-generated
-
-EXTRA_DIST = \
-	stamp-generated
-
-DISTCLEANFILES = $(ANTLR_STUFF)
-distclean-local:
-	-$(AM_V_at)rmdir generated
-	-$(AM_V_at)rm -f stamp-generated
-
-stamp-generated:
-	$(AM_V_at)mkdir -p generated
-	$(AM_V_at)touch stamp-generated
-
-# antlr doesn't overwrite output files, it just leaves them.  So we have to delete them first.
-@builddir@/TptpLexer.h: Tptp.g stamp-generated
-	-$(AM_V_at)rm -f $(ANTLR_STUFF)
-	@if test -z "$(ANTLR)"; then echo "ERROR: antlr parser generator cannot be found, cannot generate the parser" >&2; exit 1; fi
-	$(AM_V_GEN)$(ANTLR) $(ANTLR_OPTS) -fo "@builddir@" "@srcdir@/Tptp.g"
-
-# These don't actually depend on TptpLexer.h, but if we're doing parallel
-# make and the lexer needs to be rebuilt, we have to keep the rules
-# from running in parallel (since the token files will be deleted &
-# recreated)
-@builddir@/TptpLexer.c @builddir@/TptpParser.h @builddir@/TptpParser.c $(ANTLR_TOKEN_STUFF): @builddir@/TptpLexer.h
diff --git a/src/prop/bvminisat/Makefile.am b/src/prop/bvminisat/Makefile.am
deleted file mode 100644
index d34a4c12c..000000000
--- a/src/prop/bvminisat/Makefile.am
+++ /dev/null
@@ -1,44 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-D __STDC_LIMIT_MACROS \
-	-D __STDC_FORMAT_MACROS \
-	-I@builddir@/../.. -I@srcdir@/../../include -I@srcdir@/ -I@srcdir@/../..
-AM_CXXFLAGS = -Wall -Wno-parentheses -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = libbvminisat.la
-libbvminisat_la_SOURCES = \
-	core/Dimacs.h \
-	core/Solver.cc \
-	core/Solver.h \
-	core/SolverTypes.h \
-	simp/SimpSolver.cc \
-	simp/SimpSolver.h \
-	mtl/Alg.h \
-	mtl/Alloc.h \
-	mtl/Heap.h \
-	mtl/IntTypes.h \
-	mtl/Map.h \
-	mtl/Queue.h \
-	mtl/Sort.h \
-	mtl/Vec.h \
-	mtl/XAlloc.h \
-	utils/Options.h \
-	bvminisat.h \
-	bvminisat.cpp
-
-EXTRA_DIST = \
-	core/Main.cc \
-	core/Makefile \
-	doc/ReleaseNotes-2.2.0.txt \
-	simp/Main.cc \
-	simp/Makefile \
-	README \
-	LICENSE \
-	mtl/config.mk \
-	mtl/template.mk \
-	utils/Options.cc \
-	utils/ParseUtils.h \
-	utils/System.h \
-	utils/System.cc \
-	Makefile
-
diff --git a/src/prop/bvminisat/core/Makefile b/src/prop/bvminisat/core/Makefile
deleted file mode 100644
index 5de1f7295..000000000
--- a/src/prop/bvminisat/core/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-EXEC      = minisat
-DEPDIR    = mtl utils
-
-include $(MROOT)/mtl/template.mk
diff --git a/src/prop/bvminisat/simp/Makefile b/src/prop/bvminisat/simp/Makefile
deleted file mode 100644
index 27b45f493..000000000
--- a/src/prop/bvminisat/simp/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-EXEC      = minisat
-DEPDIR    = mtl utils core
-
-include $(MROOT)/mtl/template.mk
diff --git a/src/prop/bvminisat/utils/Makefile b/src/prop/bvminisat/utils/Makefile
deleted file mode 100644
index 204cea541..000000000
--- a/src/prop/bvminisat/utils/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-EXEC      = system_test
-DEPDIR    = mtl
-
-include $(MROOT)/mtl/template.mk
diff --git a/src/prop/minisat/Makefile.am b/src/prop/minisat/Makefile.am
deleted file mode 100644
index 4c110980d..000000000
--- a/src/prop/minisat/Makefile.am
+++ /dev/null
@@ -1,44 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-D __STDC_LIMIT_MACROS \
-	-D __STDC_FORMAT_MACROS \
-	-I@builddir@/../.. -I@srcdir@/../../include -I@srcdir@/ -I@srcdir@/../..
-AM_CXXFLAGS = -Wall -Wno-parentheses -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = libminisat.la
-libminisat_la_SOURCES = \
-	core/Dimacs.h \
-	core/Solver.cc \
-	core/Solver.h \
-	core/SolverTypes.h \
-	simp/SimpSolver.cc \
-	simp/SimpSolver.h \
-	mtl/Alg.h \
-	mtl/Alloc.h \
-	mtl/Heap.h \
-	mtl/IntTypes.h \
-	mtl/Map.h \
-	mtl/Queue.h \
-	mtl/Sort.h \
-	mtl/Vec.h \
-	mtl/XAlloc.h \
-	utils/Options.h \
-	minisat.cpp \
-	minisat.h
-
-EXTRA_DIST = \
-	core/Main.cc \
-	core/Makefile \
-	doc/ReleaseNotes-2.2.0.txt \
-	simp/Main.cc \
-	simp/Makefile \
-	README \
-	LICENSE \
-	mtl/config.mk \
-	mtl/template.mk \
-	utils/Options.cc \
-	utils/ParseUtils.h \
-	utils/System.h \
-	utils/System.cc \
-	Makefile
-
diff --git a/src/prop/minisat/core/Makefile b/src/prop/minisat/core/Makefile
deleted file mode 100644
index 5de1f7295..000000000
--- a/src/prop/minisat/core/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-EXEC      = minisat
-DEPDIR    = mtl utils
-
-include $(MROOT)/mtl/template.mk
diff --git a/src/prop/minisat/simp/Makefile b/src/prop/minisat/simp/Makefile
deleted file mode 100644
index 27b45f493..000000000
--- a/src/prop/minisat/simp/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-EXEC      = minisat
-DEPDIR    = mtl utils core
-
-include $(MROOT)/mtl/template.mk
diff --git a/src/prop/minisat/utils/Makefile b/src/prop/minisat/utils/Makefile
deleted file mode 100644
index 204cea541..000000000
--- a/src/prop/minisat/utils/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-EXEC      = system_test
-DEPDIR    = mtl
-
-include $(MROOT)/mtl/template.mk
diff --git a/src/smt_util/Makefile.am b/src/smt_util/Makefile.am
deleted file mode 100644
index 46f6493a9..000000000
--- a/src/smt_util/Makefile.am
+++ /dev/null
@@ -1,20 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = libsmtutil.la
-
-libsmtutil_la_SOURCES = \
-	Makefile.am \
-	Makefile.in \
-	boolean_simplification.cpp \
-	boolean_simplification.h \
-	lemma_channels.cpp \
-	lemma_channels.h \
-	lemma_input_channel.h \
-	lemma_output_channel.h \
-	nary_builder.cpp \
-	nary_builder.h \
-	node_visitor.h
-
diff --git a/src/theory/.gitignore b/src/theory/.gitignore
deleted file mode 100644
index 4d15f70c0..000000000
--- a/src/theory/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/theoryof_table.h
diff --git a/src/theory/sets/.gitignore b/src/theory/sets/.gitignore
deleted file mode 100644
index 4c83ffd6f..000000000
--- a/src/theory/sets/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-README.WHATS-NEXT
diff --git a/src/util/Makefile b/src/util/Makefile
deleted file mode 100644
index ea9087049..000000000
--- a/src/util/Makefile
+++ /dev/null
@@ -1,4 +0,0 @@
-topdir = ../..
-srcdir = src/util
-
-include $(topdir)/Makefile.subdir
diff --git a/src/util/Makefile.am b/src/util/Makefile.am
deleted file mode 100644
index baa3286ab..000000000
--- a/src/util/Makefile.am
+++ /dev/null
@@ -1,118 +0,0 @@
-AM_CPPFLAGS = \
-	-D__BUILDING_CVC4LIB \
-	-I@builddir@/.. -I@srcdir@/../include -I@srcdir@/..
-AM_CXXFLAGS = -Wall -Wno-unknown-pragmas $(FLAG_VISIBILITY_HIDDEN)
-
-noinst_LTLIBRARIES = libutil.la
-
-
-# Do not list built sources (like integer.h, rational.h) here!
-# Rather, list them under BUILT_SOURCES, and their .in versions under
-# EXTRA_DIST.  Otherwise, they're packaged up in the tarball, which is
-# no good---they belong in the configured builds/ directory.  If they
-# end up in the source directory, they build the cvc4 that was
-# configured at the time of the "make dist", which (1) may not be the
-# configuration that the user wants, and (2) might cause link errors.
-libutil_la_SOURCES = \
-	Makefile.am \
-	Makefile.in \
-	abstract_value.cpp \
-	abstract_value.h \
-	bin_heap.h \
-	bitvector.cpp \
-	bitvector.h \
-	bool.h \
-	cardinality.cpp \
-	cardinality.h \
-	channel.h \
-	debug.h \
-	dense_map.h \
-	divisible.cpp \
-	divisible.h \
-	floatingpoint.cpp \
-	gmp_util.h \
-	hash.h \
-	index.cpp \
-	index.h \
-	maybe.h \
-	ostream_util.cpp \
-	ostream_util.h \
-	proof.h \
-	random.cpp \
-	random.h \
-	regexp.cpp \
-	regexp.h \
-	resource_manager.cpp \
-	resource_manager.h \
-	result.cpp \
-	result.h \
-	safe_print.cpp \
-	safe_print.h \
-	sampler.cpp \
-	sampler.h \
-	sexpr.cpp \
-	sexpr.h \
-	smt2_quote_string.cpp \
-	smt2_quote_string.h \
-	statistics.cpp \
-	statistics.h \
-	statistics_registry.cpp \
-	statistics_registry.h \
-	tuple.h \
-	unsafe_interrupt_exception.h \
-	utility.h
-
-BUILT_SOURCES = \
-	floatingpoint.h \
-	integer.h \
-	rational.h
-
-if CVC4_CLN_IMP
-libutil_la_SOURCES += \
-	rational_cln_imp.cpp \
-	integer_cln_imp.cpp
-endif
-if CVC4_GMP_IMP
-libutil_la_SOURCES += \
-	rational_gmp_imp.cpp \
-	integer_gmp_imp.cpp
-endif
-
-
-EXTRA_DIST = \
-	bitvector.i \
-	bool.i \
-	cardinality.i \
-	divisible.i \
-	floatingpoint.h.in \
-	floatingpoint.i \
-	hash.i \
-	integer.h.in \
-	integer.i \
-	integer_cln_imp.cpp \
-	integer_cln_imp.h \
-	integer_gmp_imp.cpp \
-	integer_gmp_imp.h \
-	proof.i \
-	rational.h.in \
-	rational.i \
-	rational_cln_imp.cpp \
-	rational_cln_imp.h \
-	rational_gmp_imp.cpp \
-	rational_gmp_imp.h \
-	regexp.i \
-	resource_manager.i \
-	result.i \
-	sexpr.i \
-	statistics.i \
-	tuple.i \
-	unsafe_interrupt_exception.i
-
-
-DISTCLEANFILES = \
-	floatingpoint.h.tmp \
-	integer.h.tmp \
-	rational.h.tmp \
-	floatingpoint.h \
-	integer.h \
-	rational.h