- Update to 2.5.0

PR:		214997
Submitted by:	mzaki@e-mail.ne.jp
Approved by:	maintainer(timeout, > 14 days)

5 files changed, 190 insertions, 68 deletions

diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile
index 9223ea5128c7..4503ed661db5 100644
--- a/biology/ncbi-blast+/Makefile
+++ b/biology/ncbi-blast+/Makefile
@@ -2,8 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	blast+
-PORTVERSION=	2.2.30
-PORTREVISION=	4
+PORTVERSION=	2.5.0
 CATEGORIES=	biology
 MASTER_SITES=	http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \
 		http://acadix.biz/Ports/distfiles/
diff --git a/biology/ncbi-blast+/distinfo b/biology/ncbi-blast+/distinfo
index 5cbdbc86906f..74aa3b15dc44 100644
--- a/biology/ncbi-blast+/distinfo
+++ b/biology/ncbi-blast+/distinfo
@@ -1,2 +1,3 @@
-SHA256 (ncbi-blast-2.2.30+-src.tar.gz) = 7baa46cf761febf2660ddd9a8f9b5b02d12a3413561a554d2f85d4628a25aaa3
-SIZE (ncbi-blast-2.2.30+-src.tar.gz) = 18937894
+TIMESTAMP = 1480648908
+SHA256 (ncbi-blast-2.5.0+-src.tar.gz) = cce122a29d309127a478353856b351914232e78a9546941781ff0a4c18ec9c54
+SIZE (ncbi-blast-2.5.0+-src.tar.gz) = 19938544
diff --git a/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top b/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top
new file mode 100644
index 000000000000..0ccfbe40632c
--- /dev/null
+++ b/biology/ncbi-blast+/files/patch-src_build-system_Makefile.in.top
@@ -0,0 +1,11 @@
+--- src/build-system/Makefile.in.top.orig	2014-11-13 01:41:55.000000000 +0900
++++ src/build-system/Makefile.in.top	2016-12-02 16:39:58.415910000 +0900
+@@ -51,7 +51,7 @@
+ 	    done
+ 	cd $(includedir0) && find * -name CVS -prune -o -print |\
+             cpio -pd $(pincludedir)
+-	$(INSTALL) -m 644 $(incdir)/* $(pincludedir)
++	cd $(incdir) && find * | cpio -pd $(pincludedir)
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+ 
+ install-gbench:
diff --git a/biology/ncbi-blast+/files/patch-src_build-system_configure b/biology/ncbi-blast+/files/patch-src_build-system_configure
index da2ce4fb374a..7dc6dcba2793 100644
--- a/biology/ncbi-blast+/files/patch-src_build-system_configure
+++ b/biology/ncbi-blast+/files/patch-src_build-system_configure
@@ -1,11 +1,11 @@
---- src/build-system/configure.orig	2015-04-27 09:51:45.000000000 -0500
-+++ src/build-system/configure	2015-04-27 09:52:01.000000000 -0500
-@@ -1606,7 +1606,7 @@
-       | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \
-       | --x-includes=* | --x-libraries=* | --with-3psw=* \
-       | --target=* | --with-runpath=* | --with-relative-runpath=* \
--      | --help | --no-create | --no-recursion)
-+      | --help | --no-create | --no-recursion | --localstatedir=* )
-       ;;
- 
-       * )
+--- src/build-system/configure.orig	2016-09-09 21:04:16.000000000 +0900
++++ src/build-system/configure	2016-12-02 15:04:04.258800000 +0900
+@@ -1715,7 +1715,7 @@
+       | --silent | --cache-file=* | -C | --config-cache | -n | --no-create \
+       | --no-recursion | --prefix=* | --exec-prefix=* | --bindir=* \
+       | --libdir=* | --includedir=* | --build=* | --host=* | --target=* \
+-      | --with-runpath=* | --with-relative-runpath=* \
++      | --with-runpath=* | --with-relative-runpath=* | --localstatedir=* \
+       | --with-experimental=* | --with-extra-action=* | --with-build-root=* \
+       | --with-fake-root=* | --with-build-root-sfx=* | --with-check=* \
+       | --with-check-tools=* | --with-ftds=[0-9]* | --with-fastcgi=[0-9]* \
diff --git a/biology/ncbi-blast+/pkg-plist b/biology/ncbi-blast+/pkg-plist
index 9ea371cff2db..d319174a3821 100644
--- a/biology/ncbi-blast+/pkg-plist
+++ b/biology/ncbi-blast+/pkg-plist
@@ -19,6 +19,7 @@ bin/project_tree_builder
 bin/psiblast
 bin/rpsblast
 bin/rpstblastn
+bin/run_with_lock
 bin/seedtop
 bin/segmasker
 bin/seqdb_demo
@@ -54,6 +55,8 @@ include/ncbi-tools++/algo/blast/api/hspstream_queue.hpp
 include/ncbi-tools++/algo/blast/api/local_blast.hpp
 include/ncbi-tools++/algo/blast/api/local_db_adapter.hpp
 include/ncbi-tools++/algo/blast/api/local_search.hpp
+include/ncbi-tools++/algo/blast/api/magicblast.hpp
+include/ncbi-tools++/algo/blast/api/magicblast_options.hpp
 include/ncbi-tools++/algo/blast/api/msa_pssm_input.hpp
 include/ncbi-tools++/algo/blast/api/objmgr_query_data.hpp
 include/ncbi-tools++/algo/blast/api/objmgrfree_query_data.hpp
@@ -90,6 +93,7 @@ include/ncbi-tools++/algo/blast/api/uniform_search.hpp
 include/ncbi-tools++/algo/blast/api/version.hpp
 include/ncbi-tools++/algo/blast/api/windowmask_filter.hpp
 include/ncbi-tools++/algo/blast/blastinput/blast_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/blast_asn1_input.hpp
 include/ncbi-tools++/algo/blast/blastinput/blast_fasta_input.hpp
 include/ncbi-tools++/algo/blast/blastinput/blast_input.hpp
 include/ncbi-tools++/algo/blast/blastinput/blast_input_aux.hpp
@@ -101,6 +105,7 @@ include/ncbi-tools++/algo/blast/blastinput/cmdline_flags.hpp
 include/ncbi-tools++/algo/blast/blastinput/deltablast_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/igblastn_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/igblastp_args.hpp
+include/ncbi-tools++/algo/blast/blastinput/magicblast_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/psiblast_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/rmblastn_args.hpp
 include/ncbi-tools++/algo/blast/blastinput/rpsblast_args.hpp
@@ -158,6 +163,7 @@ include/ncbi-tools++/algo/blast/core/greedy_align.h
 include/ncbi-tools++/algo/blast/core/hspfilter_besthit.h
 include/ncbi-tools++/algo/blast/core/hspfilter_collector.h
 include/ncbi-tools++/algo/blast/core/hspfilter_culling.h
+include/ncbi-tools++/algo/blast/core/hspfilter_mapper.h
 include/ncbi-tools++/algo/blast/core/link_hsps.h
 include/ncbi-tools++/algo/blast/core/lookup_util.h
 include/ncbi-tools++/algo/blast/core/lookup_wrap.h
@@ -182,6 +188,7 @@ include/ncbi-tools++/algo/blast/format/blastxml_format.hpp
 include/ncbi-tools++/algo/blast/format/build_archive.hpp
 include/ncbi-tools++/algo/blast/format/data4xml2format.hpp
 include/ncbi-tools++/algo/blast/format/data4xmlformat.hpp
+include/ncbi-tools++/algo/blast/format/sam.hpp
 include/ncbi-tools++/algo/blast/format/vecscreen_run.hpp
 include/ncbi-tools++/algo/blast/igblast/igblast.hpp
 include/ncbi-tools++/algo/dustmask/sdust.tex
@@ -211,6 +218,7 @@ include/ncbi-tools++/algo/winmask/seq_masker_uset_array.hpp
 include/ncbi-tools++/algo/winmask/seq_masker_uset_hash.hpp
 include/ncbi-tools++/algo/winmask/seq_masker_uset_simple.hpp
 include/ncbi-tools++/algo/winmask/seq_masker_util.hpp
+include/ncbi-tools++/algo/winmask/seq_masker_version.hpp
 include/ncbi-tools++/algo/winmask/seq_masker_window.hpp
 include/ncbi-tools++/algo/winmask/seq_masker_window_ambig.hpp
 include/ncbi-tools++/algo/winmask/seq_masker_window_pattern.hpp
@@ -221,8 +229,6 @@ include/ncbi-tools++/algo/winmask/win_mask_dup_table.hpp
 include/ncbi-tools++/algo/winmask/win_mask_gen_counts.hpp
 include/ncbi-tools++/algo/winmask/win_mask_util.hpp
 include/ncbi-tools++/cgi/caf.hpp
-include/ncbi-tools++/cgi/caf_encoded.hpp
-include/ncbi-tools++/cgi/caf_plain.hpp
 include/ncbi-tools++/cgi/cgi_exception.hpp
 include/ncbi-tools++/cgi/cgi_serial.hpp
 include/ncbi-tools++/cgi/cgi_session.hpp
@@ -237,13 +243,15 @@ include/ncbi-tools++/cgi/ncbicgir.hpp
 include/ncbi-tools++/cgi/ncbires.hpp
 include/ncbi-tools++/cgi/ref_args.hpp
 include/ncbi-tools++/cgi/user_agent.hpp
+include/ncbi-tools++/common/boost_skew_guard.hpp
 include/ncbi-tools++/common/config/ncbiconf_msvc.h
-include/ncbi-tools++/common/config/ncbiconf_msvc_site.h
 include/ncbi-tools++/common/config/ncbiconf_universal.h
 include/ncbi-tools++/common/config/ncbiconf_xcode.h
-include/ncbi-tools++/common/config/ncbiconf_xcode_site.h
 include/ncbi-tools++/common/header_template.hpp
 include/ncbi-tools++/common/metamodules_doxygen.h
+include/ncbi-tools++/common/ncbi_build_ver.h
+include/ncbi-tools++/common/ncbi_build_ver.h.in
+include/ncbi-tools++/common/ncbi_build_ver.h.last
 include/ncbi-tools++/common/ncbi_export.h
 include/ncbi-tools++/common/ncbi_package_ver.h
 include/ncbi-tools++/common/ncbi_pch_impl.hpp
@@ -256,12 +264,6 @@ include/ncbi-tools++/common/test_data_path.h
 include/ncbi-tools++/connect/connect_export.h
 include/ncbi-tools++/connect/email_diag_handler.hpp
 include/ncbi-tools++/connect/error_codes.hpp
-include/ncbi-tools++/connect/ext/ncbi_crypt.h
-include/ncbi-tools++/connect/ext/ncbi_dblb.h
-include/ncbi-tools++/connect/ext/ncbi_dblb_svcmapper.hpp
-include/ncbi-tools++/connect/ext/ncbi_ifconf.h
-include/ncbi-tools++/connect/ext/ncbi_iprange.h
-include/ncbi-tools++/connect/ext/ncbi_localnet.h
 include/ncbi-tools++/connect/impl/server_connection.hpp
 include/ncbi-tools++/connect/impl/thread_pool_for_server.hpp
 include/ncbi-tools++/connect/ncbi_base64.h
@@ -282,8 +284,10 @@ include/ncbi-tools++/connect/ncbi_heapmgr.h
 include/ncbi-tools++/connect/ncbi_host_info.h
 include/ncbi-tools++/connect/ncbi_http_connector.h
 include/ncbi-tools++/connect/ncbi_http_session.hpp
+include/ncbi-tools++/connect/ncbi_lbos.hpp
 include/ncbi-tools++/connect/ncbi_memory_connector.h
 include/ncbi-tools++/connect/ncbi_misc.hpp
+include/ncbi-tools++/connect/ncbi_monkey.hpp
 include/ncbi-tools++/connect/ncbi_namedpipe.hpp
 include/ncbi-tools++/connect/ncbi_namedpipe_connector.hpp
 include/ncbi-tools++/connect/ncbi_pipe.hpp
@@ -309,11 +313,14 @@ include/ncbi-tools++/connect/services/error_codes.hpp
 include/ncbi-tools++/connect/services/grid_app_version_info.hpp
 include/ncbi-tools++/connect/services/grid_client.hpp
 include/ncbi-tools++/connect/services/grid_client_app.hpp
-include/ncbi-tools++/connect/services/grid_control_thread.hpp
 include/ncbi-tools++/connect/services/grid_globals.hpp
 include/ncbi-tools++/connect/services/grid_rw_impl.hpp
 include/ncbi-tools++/connect/services/grid_worker.hpp
 include/ncbi-tools++/connect/services/grid_worker_app.hpp
+include/ncbi-tools++/connect/services/impl/neticache_client_int.hpp
+include/ncbi-tools++/connect/services/impl/netschedule_api_int.hpp
+include/ncbi-tools++/connect/services/impl/netstorage_impl.hpp
+include/ncbi-tools++/connect/services/impl/netstorage_int.hpp
 include/ncbi-tools++/connect/services/json_over_uttp.hpp
 include/ncbi-tools++/connect/services/named_parameters.hpp
 include/ncbi-tools++/connect/services/netcache_admin.hpp
@@ -329,7 +336,7 @@ include/ncbi-tools++/connect/services/netservice_api.hpp
 include/ncbi-tools++/connect/services/netservice_api_expt.hpp
 include/ncbi-tools++/connect/services/netservice_protocol_parser.hpp
 include/ncbi-tools++/connect/services/netstorage.hpp
-include/ncbi-tools++/connect/services/netstorage_admin.hpp
+include/ncbi-tools++/connect/services/netstorage_ft.hpp
 include/ncbi-tools++/connect/services/netstorage_impl.hpp
 include/ncbi-tools++/connect/services/ns_client_factory.hpp
 include/ncbi-tools++/connect/services/ns_job_serializer.hpp
@@ -337,7 +344,6 @@ include/ncbi-tools++/connect/services/ns_output_parser.hpp
 include/ncbi-tools++/connect/services/remote_app.hpp
 include/ncbi-tools++/connect/services/srv_connections.hpp
 include/ncbi-tools++/connect/services/srv_connections_expt.hpp
-include/ncbi-tools++/connect/services/timeline.hpp
 include/ncbi-tools++/connect/services/util.hpp
 include/ncbi-tools++/connect/threaded_server.hpp
 include/ncbi-tools++/corelib/blob_storage.hpp
@@ -355,10 +361,12 @@ include/ncbi-tools++/corelib/hash_impl/_relops_hash_cont.h
 include/ncbi-tools++/corelib/hash_impl/stlp_defs.hpp
 include/ncbi-tools++/corelib/hash_map.hpp
 include/ncbi-tools++/corelib/hash_set.hpp
+include/ncbi-tools++/corelib/impl/listener_stack.hpp
 include/ncbi-tools++/corelib/impl/ncbi_atomic_defs.h
 include/ncbi-tools++/corelib/impl/ncbi_dbsvcmapper.hpp
 include/ncbi-tools++/corelib/impl/ncbi_java.h
 include/ncbi-tools++/corelib/impl/ncbi_os_mswin.h
+include/ncbi-tools++/corelib/impl/ncbi_panfs.h
 include/ncbi-tools++/corelib/impl/ncbi_param_impl.hpp
 include/ncbi-tools++/corelib/impl/ncbi_toolkit_impl.hpp
 include/ncbi-tools++/corelib/impl/ncbierror_impl.hpp
@@ -377,6 +385,7 @@ include/ncbi-tools++/corelib/ncbi_cookies.hpp
 include/ncbi-tools++/corelib/ncbi_limits.h
 include/ncbi-tools++/corelib/ncbi_limits.hpp
 include/ncbi-tools++/corelib/ncbi_mask.hpp
+include/ncbi-tools++/corelib/ncbi_message.hpp
 include/ncbi-tools++/corelib/ncbi_os_mswin.hpp
 include/ncbi-tools++/corelib/ncbi_os_unix.hpp
 include/ncbi-tools++/corelib/ncbi_param.hpp
@@ -396,6 +405,7 @@ include/ncbi-tools++/corelib/ncbiatomic.h
 include/ncbi-tools++/corelib/ncbiatomic.hpp
 include/ncbi-tools++/corelib/ncbicfg.h
 include/ncbi-tools++/corelib/ncbicntr.hpp
+include/ncbi-tools++/corelib/ncbictype.hpp
 include/ncbi-tools++/corelib/ncbidbg.hpp
 include/ncbi-tools++/corelib/ncbidiag.hpp
 include/ncbi-tools++/corelib/ncbidiag.inl
@@ -464,8 +474,10 @@ include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/odbcinst.h
 include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/sql.h
 include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/sqlext.h
 include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/sqlfront.h
+include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/sqlspi.h
 include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/sqltypes.h
 include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/sqlucode.h
+include/ncbi-tools++/dbapi/driver/odbc/unix_odbc/unixodbc_conf.h
 include/ncbi-tools++/dbapi/driver/public.hpp
 include/ncbi-tools++/dbapi/driver/types.hpp
 include/ncbi-tools++/dbapi/driver/util/blobstore.hpp
@@ -492,6 +504,7 @@ include/ncbi-tools++/html/page.hpp
 include/ncbi-tools++/html/pager.hpp
 include/ncbi-tools++/html/selection.hpp
 include/ncbi-tools++/html/writer_htmlenc.hpp
+include/ncbi-tools++/misc/error_codes.hpp
 include/ncbi-tools++/ncbi_pch.hpp
 include/ncbi-tools++/ncbi_source_ver.h
 include/ncbi-tools++/ncbiconf.h
@@ -585,16 +598,6 @@ include/ncbi-tools++/objects/biotree/Node_.hpp
 include/ncbi-tools++/objects/biotree/biotree__.hpp
 include/ncbi-tools++/objects/blast/.cvsignore
 include/ncbi-tools++/objects/blast/.cvsignore.extra
-include/ncbi-tools++/objects/blast/Bla_com_opt_db_res_by_orga.hpp
-include/ncbi-tools++/objects/blast/Bla_com_opt_db_res_by_orga_.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_disco_megab.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_disco_megab_.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_nucle_query.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_nucle_query_.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_query_filte.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_query_filte_.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_repea_filte.hpp
-include/ncbi-tools++/objects/blast/Blas_comm_opti_repea_filte_.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reply_.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_resul_reque.hpp
@@ -609,14 +612,10 @@ include/ncbi-tools++/objects/blast/Blas_get_searc_strat_reque.hpp
 include/ncbi-tools++/objects/blast/Blas_get_searc_strat_reque_.hpp
 include/ncbi-tools++/objects/blast/Blas_get_windo_taxid_reply.hpp
 include/ncbi-tools++/objects/blast/Blas_get_windo_taxid_reply_.hpp
-include/ncbi-tools++/objects/blast/Blas_queu_searc_reque_lite.hpp
-include/ncbi-tools++/objects/blast/Blas_queu_searc_reque_lite_.hpp
 include/ncbi-tools++/objects/blast/Blast4_alignment_for_query.hpp
 include/ncbi-tools++/objects/blast/Blast4_alignment_for_query_.hpp
 include/ncbi-tools++/objects/blast/Blast4_archive.hpp
 include/ncbi-tools++/objects/blast/Blast4_archive_.hpp
-include/ncbi-tools++/objects/blast/Blast4_common_options.hpp
-include/ncbi-tools++/objects/blast/Blast4_common_options_.hpp
 include/ncbi-tools++/objects/blast/Blast4_cutoff.hpp
 include/ncbi-tools++/objects/blast/Blast4_cutoff_.hpp
 include/ncbi-tools++/objects/blast/Blast4_database.hpp
@@ -659,8 +658,6 @@ include/ncbi-tools++/objects/blast/Blast4_mask.hpp
 include/ncbi-tools++/objects/blast/Blast4_mask_.hpp
 include/ncbi-tools++/objects/blast/Blast4_matrix_id.hpp
 include/ncbi-tools++/objects/blast/Blast4_matrix_id_.hpp
-include/ncbi-tools++/objects/blast/Blast4_options_lite.hpp
-include/ncbi-tools++/objects/blast/Blast4_options_lite_.hpp
 include/ncbi-tools++/objects/blast/Blast4_parameter.hpp
 include/ncbi-tools++/objects/blast/Blast4_parameter_.hpp
 include/ncbi-tools++/objects/blast/Blast4_parameter_info.hpp
@@ -707,10 +704,6 @@ include/ncbi-tools++/objects/blast/Blast4_task_info.hpp
 include/ncbi-tools++/objects/blast/Blast4_task_info_.hpp
 include/ncbi-tools++/objects/blast/Blast4_value.hpp
 include/ncbi-tools++/objects/blast/Blast4_value_.hpp
-include/ncbi-tools++/objects/blast/Blast_commo_optio_db_restr.hpp
-include/ncbi-tools++/objects/blast/Blast_commo_optio_db_restr_.hpp
-include/ncbi-tools++/objects/blast/Blast_common_option_scorin.hpp
-include/ncbi-tools++/objects/blast/Blast_common_option_scorin_.hpp
 include/ncbi-tools++/objects/blast/Blast_finish_params_reques.hpp
 include/ncbi-tools++/objects/blast/Blast_finish_params_reques_.hpp
 include/ncbi-tools++/objects/blast/Blast_get_databa_ex_reques.hpp
@@ -763,8 +756,11 @@ include/ncbi-tools++/objects/blastxml/Parameters_.hpp
 include/ncbi-tools++/objects/blastxml/Statistics.hpp
 include/ncbi-tools++/objects/blastxml/Statistics_.hpp
 include/ncbi-tools++/objects/blastxml/blastxml__.hpp
-include/ncbi-tools++/objects/blastxml2/BlastOutput.hpp
-include/ncbi-tools++/objects/blastxml2/BlastOutput_.hpp
+include/ncbi-tools++/objects/blastxml2/.cvsignore
+include/ncbi-tools++/objects/blastxml2/BlastOutput2.hpp
+include/ncbi-tools++/objects/blastxml2/BlastOutput2_.hpp
+include/ncbi-tools++/objects/blastxml2/BlastXML2.hpp
+include/ncbi-tools++/objects/blastxml2/BlastXML2_.hpp
 include/ncbi-tools++/objects/blastxml2/Err.hpp
 include/ncbi-tools++/objects/blastxml2/Err_.hpp
 include/ncbi-tools++/objects/blastxml2/Hit.hpp
@@ -775,7 +771,7 @@ include/ncbi-tools++/objects/blastxml2/Hsp.hpp
 include/ncbi-tools++/objects/blastxml2/Hsp_.hpp
 include/ncbi-tools++/objects/blastxml2/Iteration.hpp
 include/ncbi-tools++/objects/blastxml2/Iteration_.hpp
-include/ncbi-tools++/objects/blastxml2/NCBI_BlastOutput_module.hpp
+include/ncbi-tools++/objects/blastxml2/NCBI_BlastOutput2_module.hpp
 include/ncbi-tools++/objects/blastxml2/Parameters.hpp
 include/ncbi-tools++/objects/blastxml2/Parameters_.hpp
 include/ncbi-tools++/objects/blastxml2/Range.hpp
@@ -1160,12 +1156,16 @@ include/ncbi-tools++/objects/genomecoll/GCClientRequest.hpp
 include/ncbi-tools++/objects/genomecoll/GCClientRequest_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClientResponse.hpp
 include/ncbi-tools++/objects/genomecoll/GCClientResponse_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_AssembliesForSequ.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_AssembliesForSequ_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_AssemblyInfo.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_AssemblyInfo_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_AssemblySequenceI_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_AttributeFlags_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_BestAssembly.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_BestAssembly_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_EquivalentAssembl_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_Error.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_Error_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyF.hpp
@@ -1174,10 +1174,14 @@ include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyR_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_FindBestAssemblyS_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBlobRe_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyBySequ_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_GetAssemblyReques_.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_SeqIdAssemblyInfo.hpp
-include/ncbi-tools++/objects/genomecoll/GCClient_SeqIdAssemblyInfo_.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse.hpp
+include/ncbi-tools++/objects/genomecoll/GCClient_GetEquivalentAsse_.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo.hpp
 include/ncbi-tools++/objects/genomecoll/GCClient_ValidateChrTypeLo_.hpp
 include/ncbi-tools++/objects/genomecoll/GC_Assemblies.hpp
@@ -1220,6 +1224,7 @@ include/ncbi-tools++/objects/genomecoll/GC_TypedSeqId.hpp
 include/ncbi-tools++/objects/genomecoll/GC_TypedSeqId_.hpp
 include/ncbi-tools++/objects/genomecoll/NCBI_GencollClient_module.hpp
 include/ncbi-tools++/objects/genomecoll/NCBI_GenomeCollection_module.hpp
+include/ncbi-tools++/objects/genomecoll/cached_assembly.hpp
 include/ncbi-tools++/objects/genomecoll/gencoll_client__.hpp
 include/ncbi-tools++/objects/genomecoll/genome_collection__.hpp
 include/ncbi-tools++/objects/genomecoll/genomic_collections_cli.hpp
@@ -1334,6 +1339,8 @@ include/ncbi-tools++/objects/id2/NCBI_ID2Access_module.hpp
 include/ncbi-tools++/objects/id2/id2__.hpp
 include/ncbi-tools++/objects/id2/id2_client.hpp
 include/ncbi-tools++/objects/id2/id2_client_.hpp
+include/ncbi-tools++/objects/id2/id2processor.hpp
+include/ncbi-tools++/objects/id2/id2processor_interface.hpp
 include/ncbi-tools++/objects/insdseq/.cvsignore
 include/ncbi-tools++/objects/insdseq/INSDAltSeqData.hpp
 include/ncbi-tools++/objects/insdseq/INSDAltSeqData_.hpp
@@ -2866,6 +2873,8 @@ include/ncbi-tools++/objects/taxon3/Taxon3_reply.hpp
 include/ncbi-tools++/objects/taxon3/Taxon3_reply_.hpp
 include/ncbi-tools++/objects/taxon3/Taxon3_request.hpp
 include/ncbi-tools++/objects/taxon3/Taxon3_request_.hpp
+include/ncbi-tools++/objects/taxon3/cached_taxon3.hpp
+include/ncbi-tools++/objects/taxon3/itaxon3.hpp
 include/ncbi-tools++/objects/taxon3/taxon3.hpp
 include/ncbi-tools++/objects/taxon3/taxon3__.hpp
 include/ncbi-tools++/objects/tinyseq/.cvsignore
@@ -2907,6 +2916,10 @@ include/ncbi-tools++/objects/trackmgr/TMgr_BlastRIDRequest.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_BlastRIDRequest_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ClientInfo_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetReply_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetRequest.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_CreateTracksetRequest_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserDataItem.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserDataItem_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_CreateUserTrackReply.hpp
@@ -2951,10 +2964,20 @@ include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReply.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReply_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReques.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_RemoveUserTrackReques_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RenameMyNCBICollectio_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_Reply.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_Reply_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_Request.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_Request_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReply_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_RetrieveTracksetReque_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_Status.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_Status_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_SupportedAssembliesRe_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextRep_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_SwitchTrackContextReq.hpp
@@ -2975,22 +2998,29 @@ include/ncbi-tools++/objects/trackmgr/TMgr_TrackAttributes.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_TrackAttributes_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_TrackItems.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_TrackItems_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_TrackSet.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_TrackSetType.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_TrackSetType_.hpp
+include/ncbi-tools++/objects/trackmgr/TMgr_TrackSet_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_TypeStat_.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest.hpp
 include/ncbi-tools++/objects/trackmgr/TMgr_ValueRequest_.hpp
 include/ncbi-tools++/objects/trackmgr/blast_client.hpp
+include/ncbi-tools++/objects/trackmgr/createtrackset_client.hpp
 include/ncbi-tools++/objects/trackmgr/createusertrack_client.hpp
 include/ncbi-tools++/objects/trackmgr/displaytrack_client.hpp
 include/ncbi-tools++/objects/trackmgr/gridrpcclient.hpp
 include/ncbi-tools++/objects/trackmgr/item_resolver_client.hpp
 include/ncbi-tools++/objects/trackmgr/removeusertrack_client.hpp
+include/ncbi-tools++/objects/trackmgr/supported_assemblies_client.hpp
 include/ncbi-tools++/objects/trackmgr/switch_context_client.hpp
 include/ncbi-tools++/objects/trackmgr/track_attrvalue_client.hpp
 include/ncbi-tools++/objects/trackmgr/trackmgr__.hpp
 include/ncbi-tools++/objects/trackmgr/trackmgr_client.hpp
 include/ncbi-tools++/objects/trackmgr/trackmgr_client_.hpp
 include/ncbi-tools++/objects/trackmgr/trackmgr_export.h
+include/ncbi-tools++/objects/trackmgr/trackset_client.hpp
 include/ncbi-tools++/objects/valerr/.cvsignore
 include/ncbi-tools++/objects/valerr/NCBI_ValErrors_module.hpp
 include/ncbi-tools++/objects/valerr/ValidErrItem.hpp
@@ -3028,6 +3058,77 @@ include/ncbi-tools++/objects/variation/VariationMethod.hpp
 include/ncbi-tools++/objects/variation/VariationMethod_.hpp
 include/ncbi-tools++/objects/variation/Variation_.hpp
 include/ncbi-tools++/objects/variation/variation__.hpp
+include/ncbi-tools++/objects/varrep/.cvsignore
+include/ncbi-tools++/objects/varrep/AaInterval.hpp
+include/ncbi-tools++/objects/varrep/AaInterval_.hpp
+include/ncbi-tools++/objects/varrep/AaLocation.hpp
+include/ncbi-tools++/objects/varrep/AaLocation_.hpp
+include/ncbi-tools++/objects/varrep/AaSite.hpp
+include/ncbi-tools++/objects/varrep/AaSiteRange.hpp
+include/ncbi-tools++/objects/varrep/AaSiteRange_.hpp
+include/ncbi-tools++/objects/varrep/AaSite_.hpp
+include/ncbi-tools++/objects/varrep/Conversion.hpp
+include/ncbi-tools++/objects/varrep/Conversion_.hpp
+include/ncbi-tools++/objects/varrep/Count.hpp
+include/ncbi-tools++/objects/varrep/Count_.hpp
+include/ncbi-tools++/objects/varrep/CtermExtension.hpp
+include/ncbi-tools++/objects/varrep/CtermExtension_.hpp
+include/ncbi-tools++/objects/varrep/Deletion.hpp
+include/ncbi-tools++/objects/varrep/Deletion_.hpp
+include/ncbi-tools++/objects/varrep/Delins.hpp
+include/ncbi-tools++/objects/varrep/Delins_.hpp
+include/ncbi-tools++/objects/varrep/Duplication.hpp
+include/ncbi-tools++/objects/varrep/Duplication_.hpp
+include/ncbi-tools++/objects/varrep/Frameshift.hpp
+include/ncbi-tools++/objects/varrep/Frameshift_.hpp
+include/ncbi-tools++/objects/varrep/Insertion.hpp
+include/ncbi-tools++/objects/varrep/Insertion_.hpp
+include/ncbi-tools++/objects/varrep/Inversion.hpp
+include/ncbi-tools++/objects/varrep/Inversion_.hpp
+include/ncbi-tools++/objects/varrep/NCBI_VariationIRep_module.hpp
+include/ncbi-tools++/objects/varrep/NaIdentity.hpp
+include/ncbi-tools++/objects/varrep/NaIdentity_.hpp
+include/ncbi-tools++/objects/varrep/NaSub.hpp
+include/ncbi-tools++/objects/varrep/NaSub_.hpp
+include/ncbi-tools++/objects/varrep/NtIntLimit.hpp
+include/ncbi-tools++/objects/varrep/NtIntLimit_.hpp
+include/ncbi-tools++/objects/varrep/NtInterval.hpp
+include/ncbi-tools++/objects/varrep/NtInterval_.hpp
+include/ncbi-tools++/objects/varrep/NtLocation.hpp
+include/ncbi-tools++/objects/varrep/NtLocation_.hpp
+include/ncbi-tools++/objects/varrep/NtSite.hpp
+include/ncbi-tools++/objects/varrep/NtSiteRange.hpp
+include/ncbi-tools++/objects/varrep/NtSiteRange_.hpp
+include/ncbi-tools++/objects/varrep/NtSite_.hpp
+include/ncbi-tools++/objects/varrep/NtermExtension.hpp
+include/ncbi-tools++/objects/varrep/NtermExtension_.hpp
+include/ncbi-tools++/objects/varrep/ProteinExtension.hpp
+include/ncbi-tools++/objects/varrep/ProteinExtension_.hpp
+include/ncbi-tools++/objects/varrep/ProteinSub.hpp
+include/ncbi-tools++/objects/varrep/ProteinSub_.hpp
+include/ncbi-tools++/objects/varrep/Repeat.hpp
+include/ncbi-tools++/objects/varrep/Repeat_.hpp
+include/ncbi-tools++/objects/varrep/SeqInterval.hpp
+include/ncbi-tools++/objects/varrep/SeqInterval_.hpp
+include/ncbi-tools++/objects/varrep/SeqLocation.hpp
+include/ncbi-tools++/objects/varrep/SeqLocation_.hpp
+include/ncbi-tools++/objects/varrep/SequenceVariant.hpp
+include/ncbi-tools++/objects/varrep/SequenceVariant_.hpp
+include/ncbi-tools++/objects/varrep/SimpleVariant.hpp
+include/ncbi-tools++/objects/varrep/SimpleVariantSeq.hpp
+include/ncbi-tools++/objects/varrep/SimpleVariantSeq_.hpp
+include/ncbi-tools++/objects/varrep/SimpleVariant_.hpp
+include/ncbi-tools++/objects/varrep/SpecialVariant.hpp
+include/ncbi-tools++/objects/varrep/SpecialVariant_.hpp
+include/ncbi-tools++/objects/varrep/Subsequence.hpp
+include/ncbi-tools++/objects/varrep/Subsequence_.hpp
+include/ncbi-tools++/objects/varrep/Variant.hpp
+include/ncbi-tools++/objects/varrep/VariantExpression.hpp
+include/ncbi-tools++/objects/varrep/VariantExpression_.hpp
+include/ncbi-tools++/objects/varrep/VariantSeqType.hpp
+include/ncbi-tools++/objects/varrep/VariantSeqType_.hpp
+include/ncbi-tools++/objects/varrep/Variant_.hpp
+include/ncbi-tools++/objects/varrep/varrep__.hpp
 include/ncbi-tools++/objmgr/align_ci.hpp
 include/ncbi-tools++/objmgr/annot_ci.hpp
 include/ncbi-tools++/objmgr/annot_name.hpp
@@ -3075,6 +3176,7 @@ include/ncbi-tools++/objmgr/impl/seq_annot_edit_commands.hpp
 include/ncbi-tools++/objmgr/impl/seq_annot_info.hpp
 include/ncbi-tools++/objmgr/impl/seq_entry_edit_commands.hpp
 include/ncbi-tools++/objmgr/impl/seq_entry_info.hpp
+include/ncbi-tools++/objmgr/impl/seq_id_sort.hpp
 include/ncbi-tools++/objmgr/impl/seq_loc_cvt.hpp
 include/ncbi-tools++/objmgr/impl/seq_table_info.hpp
 include/ncbi-tools++/objmgr/impl/seq_table_setter.hpp
@@ -3084,6 +3186,7 @@ include/ncbi-tools++/objmgr/impl/seq_vector_cvt_gcc_i386.hpp
 include/ncbi-tools++/objmgr/impl/seq_vector_cvt_gen.hpp
 include/ncbi-tools++/objmgr/impl/snp_annot_info.hpp
 include/ncbi-tools++/objmgr/impl/snp_info.hpp
+include/ncbi-tools++/objmgr/impl/split_parser.hpp
 include/ncbi-tools++/objmgr/impl/synonyms.hpp
 include/ncbi-tools++/objmgr/impl/tse_assigner.hpp
 include/ncbi-tools++/objmgr/impl/tse_chunk_info.hpp
@@ -3137,6 +3240,7 @@ include/ncbi-tools++/objmgr/unsupp_editsaver.hpp
 include/ncbi-tools++/objmgr/util/create_defline.hpp
 include/ncbi-tools++/objmgr/util/feature.hpp
 include/ncbi-tools++/objmgr/util/obj_sniff.hpp
+include/ncbi-tools++/objmgr/util/objutil.hpp
 include/ncbi-tools++/objmgr/util/seq_align_util.hpp
 include/ncbi-tools++/objmgr/util/seq_loc_util.hpp
 include/ncbi-tools++/objmgr/util/sequence.hpp
@@ -3149,6 +3253,7 @@ include/ncbi-tools++/objtools/align_format/seqalignfilter.hpp
 include/ncbi-tools++/objtools/align_format/showalign.hpp
 include/ncbi-tools++/objtools/align_format/showdefline.hpp
 include/ncbi-tools++/objtools/align_format/tabular.hpp
+include/ncbi-tools++/objtools/align_format/taxFormat.hpp
 include/ncbi-tools++/objtools/align_format/vectorscreen.hpp
 include/ncbi-tools++/objtools/alnmgr/aln_asn_reader.hpp
 include/ncbi-tools++/objtools/alnmgr/aln_builders.hpp
@@ -3247,15 +3352,8 @@ include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id1_base.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/reader_service.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/request_result.hpp
-include/ncbi-tools++/objtools/data_loaders/genbank/impl/split_parser.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/standalone_result.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/impl/statistics.hpp
-include/ncbi-tools++/objtools/data_loaders/genbank/pubseq/reader_pubseq.hpp
-include/ncbi-tools++/objtools/data_loaders/genbank/pubseq/reader_pubseq_entry.hpp
-include/ncbi-tools++/objtools/data_loaders/genbank/pubseq/reader_pubseq_params.h
-include/ncbi-tools++/objtools/data_loaders/genbank/pubseq2/reader_pubseq2.hpp
-include/ncbi-tools++/objtools/data_loaders/genbank/pubseq2/reader_pubseq2_entry.hpp
-include/ncbi-tools++/objtools/data_loaders/genbank/pubseq2/reader_pubseq2_params.h
 include/ncbi-tools++/objtools/data_loaders/genbank/reader.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/reader_interface.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/reader_params.h
@@ -3272,11 +3370,13 @@ include/ncbi-tools++/objtools/data_loaders/genbank/seqref.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/writer.hpp
 include/ncbi-tools++/objtools/data_loaders/genbank/writer_interface.hpp
 include/ncbi-tools++/objtools/data_loaders/loaders.hpp
+include/ncbi-tools++/objtools/edit/apply_object.hpp
 include/ncbi-tools++/objtools/edit/autodef.hpp
 include/ncbi-tools++/objtools/edit/autodef_available_modifier.hpp
 include/ncbi-tools++/objtools/edit/autodef_feature_clause.hpp
 include/ncbi-tools++/objtools/edit/autodef_feature_clause_base.hpp
 include/ncbi-tools++/objtools/edit/autodef_mod_combo.hpp
+include/ncbi-tools++/objtools/edit/autodef_options.hpp
 include/ncbi-tools++/objtools/edit/autodef_source_desc.hpp
 include/ncbi-tools++/objtools/edit/autodef_source_group.hpp
 include/ncbi-tools++/objtools/edit/capitalization_string.hpp
@@ -3291,9 +3391,14 @@ include/ncbi-tools++/objtools/edit/gene_utils.hpp
 include/ncbi-tools++/objtools/edit/link_cds_mrna.hpp
 include/ncbi-tools++/objtools/edit/loc_edit.hpp
 include/ncbi-tools++/objtools/edit/mail_report.hpp
+include/ncbi-tools++/objtools/edit/parse_text_options.hpp
 include/ncbi-tools++/objtools/edit/promote.hpp
+include/ncbi-tools++/objtools/edit/publication_edit.hpp
+include/ncbi-tools++/objtools/edit/remote_updater.hpp
+include/ncbi-tools++/objtools/edit/rna_edit.hpp
 include/ncbi-tools++/objtools/edit/seq_entry_edit.hpp
 include/ncbi-tools++/objtools/edit/seqid_guesser.hpp
+include/ncbi-tools++/objtools/edit/source_edit.hpp
 include/ncbi-tools++/objtools/edit/string_constraint.hpp
 include/ncbi-tools++/objtools/edit/struc_comm_field.hpp
 include/ncbi-tools++/objtools/edit/text_desc_field.hpp
@@ -3391,6 +3496,7 @@ include/ncbi-tools++/objtools/readers/rm_reader.hpp
 include/ncbi-tools++/objtools/readers/source_mod_parser.hpp
 include/ncbi-tools++/objtools/readers/source_mod_parser_wrapper.hpp
 include/ncbi-tools++/objtools/readers/table_filter.hpp
+include/ncbi-tools++/objtools/readers/track_data.hpp
 include/ncbi-tools++/objtools/readers/ucscregion_reader.hpp
 include/ncbi-tools++/objtools/readers/vcf_reader.hpp
 include/ncbi-tools++/objtools/readers/wiggle_reader.hpp
@@ -3488,6 +3594,7 @@ include/ncbi-tools++/serial/objostrjson.hpp
 include/ncbi-tools++/serial/objostrxml.hpp
 include/ncbi-tools++/serial/pack_string.hpp
 include/ncbi-tools++/serial/rpcbase.hpp
+include/ncbi-tools++/serial/rpcbase_impl.hpp
 include/ncbi-tools++/serial/serial.hpp
 include/ncbi-tools++/serial/serialasn.hpp
 include/ncbi-tools++/serial/serialbase.hpp
@@ -3558,6 +3665,7 @@ include/ncbi-tools++/util/dictionary.hpp
 include/ncbi-tools++/util/dictionary_util.hpp
 include/ncbi-tools++/util/distribution.hpp
 include/ncbi-tools++/util/error_codes.hpp
+include/ncbi-tools++/util/file_manifest.hpp
 include/ncbi-tools++/util/file_obsolete.hpp
 include/ncbi-tools++/util/floating_point.hpp
 include/ncbi-tools++/util/format_guess.hpp
@@ -3588,6 +3696,7 @@ include/ncbi-tools++/util/ncbi_url.hpp
 include/ncbi-tools++/util/random_gen.hpp
 include/ncbi-tools++/util/range.hpp
 include/ncbi-tools++/util/range_coll.hpp
+include/ncbi-tools++/util/rangelist.hpp
 include/ncbi-tools++/util/rangemap.hpp
 include/ncbi-tools++/util/rangemap.inl
 include/ncbi-tools++/util/reader_writer.hpp
@@ -3599,6 +3708,7 @@ include/ncbi-tools++/util/regexp/pcreposix.h
 include/ncbi-tools++/util/request_control.hpp
 include/ncbi-tools++/util/resize_iter.hpp
 include/ncbi-tools++/util/resource_pool.hpp
+include/ncbi-tools++/util/retry_ctx.hpp
 include/ncbi-tools++/util/scheduler.hpp
 include/ncbi-tools++/util/sequtil/sequtil.hpp
 include/ncbi-tools++/util/sequtil/sequtil_convert.hpp
@@ -3611,6 +3721,7 @@ include/ncbi-tools++/util/static_map.hpp
 include/ncbi-tools++/util/static_set.hpp
 include/ncbi-tools++/util/strbuffer.hpp
 include/ncbi-tools++/util/strbuffer.inl
+include/ncbi-tools++/util/stream_source.hpp
 include/ncbi-tools++/util/strsearch.hpp
 include/ncbi-tools++/util/sync_queue.hpp
 include/ncbi-tools++/util/table_printer.hpp
@@ -3622,6 +3733,7 @@ include/ncbi-tools++/util/thread_pool.hpp
 include/ncbi-tools++/util/thread_pool_ctrl.hpp
 include/ncbi-tools++/util/thread_pool_old.hpp
 include/ncbi-tools++/util/time_line.hpp
+include/ncbi-tools++/util/timsort.hpp
 include/ncbi-tools++/util/transmissionrw.hpp
 include/ncbi-tools++/util/unicode.hpp
 include/ncbi-tools++/util/utf8.hpp
@@ -3635,6 +3747,7 @@ include/ncbi-tools++/util/weakmap.inl
 include/ncbi-tools++/util/xregexp/arg_regexp.hpp
 include/ncbi-tools++/util/xregexp/mask_regexp.hpp
 include/ncbi-tools++/util/xregexp/regexp.hpp
+include/ncbi-tools++/util/xregexp/regexp_template_tester.hpp
 lib/libaccess-static.a
 lib/libaccess.a
 lib/libalign_format-static.a
@@ -3667,8 +3780,6 @@ lib/libcomposition_adjustment-static.a
 lib/libcomposition_adjustment.a
 lib/libconnect-static.a
 lib/libconnect.a
-lib/libconnext-static.a
-lib/libconnext.a
 lib/libconnssl-static.a
 lib/libconnssl.a
 lib/libcreaders-static.a
@@ -3820,14 +3931,14 @@ lib/libtrackmgr-static.a
 lib/libtrackmgr.a
 lib/libtrackmgrcli-static.a
 lib/libtrackmgrcli.a
-lib/libtrackmgrgridcli-static.a
-lib/libtrackmgrgridcli.a
 lib/libvalerr-static.a
 lib/libvalerr.a
 lib/libvalid-static.a
 lib/libvalid.a
 lib/libvariation-static.a
 lib/libvariation.a
+lib/libvarrep-static.a
+lib/libvarrep.a
 lib/libwritedb-static.a
 lib/libwritedb.a
 lib/libxalgoblastdbindex-static.a
@@ -3852,8 +3963,6 @@ lib/libxcompress-static.a
 lib/libxcompress.a
 lib/libxconnect-static.a
 lib/libxconnect.a
-lib/libxconnext-static.a
-lib/libxconnext.a
 lib/libxconnserv-static.a
 lib/libxconnserv.a
 lib/libxcser-static.a
@@ -3884,6 +3993,8 @@ lib/libxobjutil-static.a
 lib/libxobjutil.a
 lib/libxregexp-static.a
 lib/libxregexp.a
+lib/libxregexp_template_tester-static.a
+lib/libxregexp_template_tester.a
 lib/libxser-static.a
 lib/libxser.a
 lib/libxthrserv-static.a