diff --git a/scripts/update_api.py b/scripts/update_api.py
index 4000b3da2..67a1b8a33 100755
--- a/scripts/update_api.py
+++ b/scripts/update_api.py
@@ -1573,7 +1573,7 @@ def def_APIs(api_files):
 
 def write_log_h_preamble(log_h):
   log_h.write('// Automatically generated file\n')
-  log_h.write('#include\"z3.h\"\n')
+  log_h.write('#include\"api/z3.h\"\n')
   log_h.write('#ifdef __GNUC__\n')
   log_h.write('#define _Z3_UNUSED __attribute__((unused))\n')
   log_h.write('#else\n')
@@ -1592,14 +1592,14 @@ def write_log_h_preamble(log_h):
 def write_log_c_preamble(log_c):
   log_c.write('// Automatically generated file\n')
   log_c.write('#include<iostream>\n')
-  log_c.write('#include\"z3.h\"\n')
-  log_c.write('#include\"api_log_macros.h\"\n')
-  log_c.write('#include\"z3_logger.h\"\n')
+  log_c.write('#include\"api/z3.h\"\n')
+  log_c.write('#include\"api/api_log_macros.h\"\n')
+  log_c.write('#include\"api/z3_logger.h\"\n')
 
 def write_exe_c_preamble(exe_c):
   exe_c.write('// Automatically generated file\n')
-  exe_c.write('#include\"z3.h\"\n')
-  exe_c.write('#include\"z3_replayer.h\"\n')
+  exe_c.write('#include\"api/z3.h\"\n')
+  exe_c.write('#include\"api/z3_replayer.h\"\n')
   #
   exe_c.write('void Z3_replayer_error_handler(Z3_context ctx, Z3_error_code c) { printf("[REPLAYER ERROR HANDLER]: %s\\n", Z3_get_error_msg(ctx, c)); }\n')
 
diff --git a/src/api/api_algebraic.cpp b/src/api/api_algebraic.cpp
index 40e8c846b..96d8392ba 100644
--- a/src/api/api_algebraic.cpp
+++ b/src/api/api_algebraic.cpp
@@ -18,7 +18,7 @@ Notes:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_ast_vector.h"
 #include "math/polynomial/algebraic_numbers.h"
diff --git a/src/api/api_arith.cpp b/src/api/api_arith.cpp
index 80eb261ad..8fbed6f46 100644
--- a/src/api/api_arith.cpp
+++ b/src/api/api_arith.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/arith_decl_plugin.h"
diff --git a/src/api/api_array.cpp b/src/api/api_array.cpp
index f4682ea8f..a5916e987 100644
--- a/src/api/api_array.cpp
+++ b/src/api/api_array.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/array_decl_plugin.h"
diff --git a/src/api/api_ast.cpp b/src/api/api_ast.cpp
index c14a24df1..ab93c3cbd 100644
--- a/src/api/api_ast.cpp
+++ b/src/api/api_ast.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include<iostream>
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/well_sorted.h"
diff --git a/src/api/api_ast_map.cpp b/src/api/api_ast_map.cpp
index fc593c1f5..d0388b97a 100644
--- a/src/api/api_ast_map.cpp
+++ b/src/api/api_ast_map.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_ast_map.h"
 #include "api/api_ast_vector.h"
diff --git a/src/api/api_ast_vector.cpp b/src/api/api_ast_vector.cpp
index 04802cba5..471a308b6 100644
--- a/src/api/api_ast_vector.cpp
+++ b/src/api/api_ast_vector.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_ast_vector.h"
 #include "ast/ast_translation.h"
diff --git a/src/api/api_bv.cpp b/src/api/api_bv.cpp
index 52fcb867c..3b5d60be3 100644
--- a/src/api/api_bv.cpp
+++ b/src/api/api_bv.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/bv_decl_plugin.h"
diff --git a/src/api/api_config_params.cpp b/src/api/api_config_params.cpp
index d35297f59..460101d34 100644
--- a/src/api/api_config_params.cpp
+++ b/src/api/api_config_params.cpp
@@ -18,7 +18,7 @@ Revision History:
 #include "api/z3.h"
 #include "api/api_context.h"
 #include "ast/pp.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_util.h"
 #include "cmd_context/cmd_context.h"
 #include "util/symbol.h"
diff --git a/src/api/api_context.cpp b/src/api/api_context.cpp
index 2c93ee85d..210e0a1d4 100644
--- a/src/api/api_context.cpp
+++ b/src/api/api_context.cpp
@@ -20,10 +20,10 @@ Revision History:
 #include<typeinfo>
 #include "api/api_context.h"
 #include "parsers/smt/smtparser.h"
-#include"version.h"
+#include "util/version.h"
 #include "ast/ast_pp.h"
 #include "ast/ast_ll_pp.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_util.h"
 #include "ast/reg_decl_plugins.h"
 #include "math/realclosure/realclosure.h"
diff --git a/src/api/api_datalog.cpp b/src/api/api_datalog.cpp
index 8f863ed42..397e2a8af 100644
--- a/src/api/api_datalog.cpp
+++ b/src/api/api_datalog.cpp
@@ -20,7 +20,7 @@ Revision History:
 #include "api/api_util.h"
 #include "ast/ast_pp.h"
 #include "api/api_ast_vector.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_stats.h"
 #include "muz/fp/datalog_parser.h"
 #include "util/cancel_eh.h"
diff --git a/src/api/api_datatype.cpp b/src/api/api_datatype.cpp
index 7e9758a04..851d96a4e 100644
--- a/src/api/api_datatype.cpp
+++ b/src/api/api_datatype.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/datatype_decl_plugin.h"
diff --git a/src/api/api_fpa.cpp b/src/api/api_fpa.cpp
index 8e4d13af4..484cb3d76 100644
--- a/src/api/api_fpa.cpp
+++ b/src/api/api_fpa.cpp
@@ -18,7 +18,7 @@ Notes:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "ast/fpa_decl_plugin.h"
 
diff --git a/src/api/api_goal.cpp b/src/api/api_goal.cpp
index 3fe23828d..0f1b9056b 100644
--- a/src/api/api_goal.cpp
+++ b/src/api/api_goal.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_goal.h"
 #include "ast/ast_translation.h"
diff --git a/src/api/api_interp.cpp b/src/api/api_interp.cpp
index 276e56989..fb2699e0a 100644
--- a/src/api/api_interp.cpp
+++ b/src/api/api_interp.cpp
@@ -18,7 +18,7 @@
 #include<sstream>
 #include<vector>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_tactic.h"
 #include "api/api_solver.h"
diff --git a/src/api/api_log.cpp b/src/api/api_log.cpp
index aa00de424..410110d9a 100644
--- a/src/api/api_log.cpp
+++ b/src/api/api_log.cpp
@@ -17,9 +17,9 @@ Revision History:
 --*/
 #include<fstream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "util/util.h"
-#include"version.h"
+#include "util/version.h"
 
 std::ostream * g_z3_log = 0;
 bool g_z3_log_enabled   = false;
diff --git a/src/api/api_model.cpp b/src/api/api_model.cpp
index 73428a3d7..de917650d 100644
--- a/src/api/api_model.cpp
+++ b/src/api/api_model.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_model.h"
 #include "api/api_ast_vector.h"
diff --git a/src/api/api_numeral.cpp b/src/api/api_numeral.cpp
index c3717b5d2..95bc0bef9 100644
--- a/src/api/api_numeral.cpp
+++ b/src/api/api_numeral.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/arith_decl_plugin.h"
diff --git a/src/api/api_opt.cpp b/src/api/api_opt.cpp
index 8c49b526e..a967dfb2b 100644
--- a/src/api/api_opt.cpp
+++ b/src/api/api_opt.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_stats.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
diff --git a/src/api/api_params.cpp b/src/api/api_params.cpp
index 86dfe9a93..3f3cbed1d 100644
--- a/src/api/api_params.cpp
+++ b/src/api/api_params.cpp
@@ -19,7 +19,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "util/params.h"
diff --git a/src/api/api_parsers.cpp b/src/api/api_parsers.cpp
index 8c2723e9a..bef31e9f1 100644
--- a/src/api/api_parsers.cpp
+++ b/src/api/api_parsers.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "cmd_context/cmd_context.h"
diff --git a/src/api/api_pb.cpp b/src/api/api_pb.cpp
index 97e627ec0..e6f8f77b4 100644
--- a/src/api/api_pb.cpp
+++ b/src/api/api_pb.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/pb_decl_plugin.h"
diff --git a/src/api/api_polynomial.cpp b/src/api/api_polynomial.cpp
index 398fdeb3a..9be73289f 100644
--- a/src/api/api_polynomial.cpp
+++ b/src/api/api_polynomial.cpp
@@ -17,7 +17,7 @@ Notes:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_polynomial.h"
 #include "api/api_ast_vector.h"
diff --git a/src/api/api_qe.cpp b/src/api/api_qe.cpp
index 0c2948ce5..34f21d64b 100644
--- a/src/api/api_qe.cpp
+++ b/src/api/api_qe.cpp
@@ -19,7 +19,7 @@ Notes:
 
 #include <iostream>
 #include "api/z3.h"
-#include "api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "api/api_model.h"
diff --git a/src/api/api_quant.cpp b/src/api/api_quant.cpp
index f7d5bf13a..d64768b3b 100644
--- a/src/api/api_quant.cpp
+++ b/src/api/api_quant.cpp
@@ -16,7 +16,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "parsers/util/pattern_validation.h"
diff --git a/src/api/api_rcf.cpp b/src/api/api_rcf.cpp
index 377e83a44..84c250114 100644
--- a/src/api/api_rcf.cpp
+++ b/src/api/api_rcf.cpp
@@ -21,7 +21,7 @@ Notes:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "math/realclosure/realclosure.h"
 
diff --git a/src/api/api_seq.cpp b/src/api/api_seq.cpp
index a652fd912..44003a5fb 100644
--- a/src/api/api_seq.cpp
+++ b/src/api/api_seq.cpp
@@ -17,7 +17,7 @@ Revision History:
 
 --*/
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_util.h"
 #include "ast/ast_pp.h"
diff --git a/src/api/api_solver.cpp b/src/api/api_solver.cpp
index 6435b8288..7fd6d08fe 100644
--- a/src/api/api_solver.cpp
+++ b/src/api/api_solver.cpp
@@ -18,7 +18,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_tactic.h"
 #include "api/api_solver.h"
diff --git a/src/api/api_stats.cpp b/src/api/api_stats.cpp
index 440aec22d..a92b908dc 100644
--- a/src/api/api_stats.cpp
+++ b/src/api/api_stats.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_stats.h"
 
diff --git a/src/api/api_tactic.cpp b/src/api/api_tactic.cpp
index 661660a63..ccb1ce597 100644
--- a/src/api/api_tactic.cpp
+++ b/src/api/api_tactic.cpp
@@ -17,7 +17,7 @@ Revision History:
 --*/
 #include<iostream>
 #include "api/z3.h"
-#include"api_log_macros.h"
+#include "api/api_log_macros.h"
 #include "api/api_context.h"
 #include "api/api_tactic.h"
 #include "api/api_model.h"
diff --git a/src/cmd_context/basic_cmds.cpp b/src/cmd_context/basic_cmds.cpp
index db522b82b..c81170ba4 100644
--- a/src/cmd_context/basic_cmds.cpp
+++ b/src/cmd_context/basic_cmds.cpp
@@ -16,7 +16,7 @@ Notes:
 
 --*/
 #include "cmd_context/cmd_context.h"
-#include"version.h"
+#include "util/version.h"
 #include "ast/ast_smt_pp.h"
 #include "ast/ast_smt2_pp.h"
 #include "ast/ast_pp.h"
diff --git a/src/duality/duality_wrapper.h b/src/duality/duality_wrapper.h
index 8e2d70ea6..8ea8017a2 100644
--- a/src/duality/duality_wrapper.h
+++ b/src/duality/duality_wrapper.h
@@ -27,7 +27,7 @@
 #include<vector>
 #include<list>
 #include <set>
-#include"version.h"
+#include "util/version.h"
 #include<limits.h>
 
 #include "interp/iz3hash.h"
diff --git a/src/shell/main.cpp b/src/shell/main.cpp
index 3f3ba5182..3d2609c4f 100644
--- a/src/shell/main.cpp
+++ b/src/shell/main.cpp
@@ -26,7 +26,7 @@ Revision History:
 #include "shell/smtlib_frontend.h"
 #include "shell/z3_log_frontend.h"
 #include "util/warning.h"
-#include"version.h"
+#include "util/version.h"
 #include "shell/dimacs_frontend.h"
 #include "shell/datalog_frontend.h"
 #include "shell/opt_frontend.h"