diff --git a/app-benchmarks/nbench/nbench-2.2.3-r2.ebuild b/app-benchmarks/nbench/nbench-2.2.3-r2.ebuild
index 2e1a44e3fbfd2..38c9465cbe97c 100644
--- a/app-benchmarks/nbench/nbench-2.2.3-r2.ebuild
+++ b/app-benchmarks/nbench/nbench-2.2.3-r2.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
 MY_P="${PN}-byte-${PV}"
 
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Linux/Unix of release 2 of BYTE Magazine's BYTEmark benchmark"
 HOMEPAGE="http://www.tux.org/~mayer/linux/bmark.html"
@@ -30,6 +30,8 @@ src_prepare() {
 
 src_configure() {
 	tc-export CC
+	# bug #943907
+	append-cflags -std=gnu17
 }
 
 src_install() {
diff --git a/app-pda/pilot-link/files/pilot-link-0.12.5-C23.patch b/app-pda/pilot-link/files/pilot-link-0.12.5-C23.patch
new file mode 100644
index 0000000000000..59e995725872a
--- /dev/null
+++ b/app-pda/pilot-link/files/pilot-link-0.12.5-C23.patch
@@ -0,0 +1,85 @@
+Correct build for C23
+Wrong type for size variable, missing parameters in decls
+Missing include and wrong types in bundled libusb library
+https://bugs.gentoo.org/944433
+https://bugs.gentoo.org/883101
+--- a/src/parsedate.c
++++ b/src/parsedate.c
+@@ -175,8 +175,8 @@
+ static time_t	yyRelSeconds;
+ 
+ 
+-extern struct tm	*localtime();
+-static void		date_error();
++extern struct tm	*localtime(const time_t *timep);
++static void		date_error(char *s);
+ 
+ 
+ /* Enabling traces.  */
+--- a/src/parsedate.y
++++ b/src/parsedate.y
+@@ -94,8 +94,8 @@
+ static time_t	yyRelSeconds;
+ 
+ 
+-extern struct tm	*localtime();
+-static void		date_error();
++extern struct tm	*localtime(const time_t *timep);
++static void		date_error(char *s);
+ %}
+ 
+ %union {
+--- a/src/pilot-read-todos.c
++++ b/src/pilot-read-todos.c
+@@ -202,8 +202,8 @@
+ 
+ 	for (i = 0;; i++) {
+ 		int 	attr,
+-			category,
+-			len;
++			category;
++		ssize_t	len;
+ 
+ 		struct 	ToDo todo;
+ 
+--- a/libpisock/linuxusb.c
++++ b/libpisock/linuxusb.c
+@@ -27,6 +27,7 @@
+ #include <stdio.h>
+ #include <sys/types.h>
+ #include <sys/stat.h>
++#include <sys/socket.h>
+ 
+ #include "pi-debug.h"
+ #include "pi-source.h"
+@@ -48,8 +49,8 @@
+ 
+ static int u_open(pi_socket_t *ps, struct pi_sockaddr *addr, size_t addrlen);
+ static int u_close(pi_socket_t *ps);
+-static int u_write(pi_socket_t *ps, unsigned char *buf, size_t len, int flags);
+-static int u_read(pi_socket_t *ps, pi_buffer_t *buf, size_t len, int flags);
++static ssize_t u_write(pi_socket_t *ps, const unsigned char *buf, size_t len, int flags);
++static ssize_t u_read(pi_socket_t *ps, pi_buffer_t *buf, size_t len, int flags);
+ static int u_poll(pi_socket_t *ps, int timeout);
+ static int u_flush(pi_socket_t *ps, int flags);
+ 
+@@ -188,8 +189,8 @@
+  * Returns:     Nothing
+  *
+  ***********************************************************************/
+-static int
+-u_write(pi_socket_t *ps, unsigned char *buf, size_t len, int flags)
++static ssize_t
++u_write(pi_socket_t *ps, const unsigned char *buf, size_t len, int flags)
+ {
+ 	int 	total,
+ 		nwrote;
+@@ -281,7 +282,7 @@
+  * Returns:     number of bytes read or negative otherwise
+  *
+  ***********************************************************************/
+-static int
++static ssize_t
+ u_read(pi_socket_t *ps, pi_buffer_t *buf, size_t len, int flags)
+ {
+ 	ssize_t rbuf = 0,
diff --git a/app-pda/pilot-link/pilot-link-0.12.5-r5.ebuild b/app-pda/pilot-link/pilot-link-0.12.5-r5.ebuild
new file mode 100644
index 0000000000000..442358fff55f8
--- /dev/null
+++ b/app-pda/pilot-link/pilot-link-0.12.5-r5.ebuild
@@ -0,0 +1,103 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit autotools flag-o-matic perl-module
+
+DESCRIPTION="Suite of tools for moving data between a Palm device and a desktop"
+# this is a new mirror; the distfile has the same content inside the tarball,
+# but the tarball itself doesn't match due to recompression and Git
+# indirection.
+HOMEPAGE="https://github.com/jichu4n/pilot-link"
+SRC_URI="
+	mirror://gentoo/${P}.tar.bz2
+	https://dev.gentoo.org/~soap/distfiles/${P}-gentoo-patchset-r2.tar.xz"
+
+LICENSE="|| ( GPL-2 LGPL-2 )"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="bluetooth perl png threads usb"
+RESTRICT="test" #672872
+
+RDEPEND="
+	dev-libs/popt
+	sys-libs/ncurses:=
+	sys-libs/readline:=
+	virtual/libiconv
+	bluetooth? ( net-wireless/bluez )
+	perl? ( dev-lang/perl:= )
+	png? ( media-libs/libpng:= )
+	usb? ( virtual/libusb:0 )"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	virtual/pkgconfig
+	perl? ( dev-lang/perl )
+	sys-devel/bison"
+
+PATCHES=(
+	"${WORKDIR}/${P}-gentoo-patchset"/
+	"${FILESDIR}/${P}-C23.patch"
+)
+
+src_prepare() {
+	default
+	eautoreconf
+}
+
+src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/924480
+	#
+	# Upstream is abandoned since 2016, existing issue offering gentoo-patchset
+	# has been ignored. No bug filed.
+	#
+	# The issue is in the internal compat code for *not* using libusb.
+	use usb || filter-lto
+
+	# tcl/tk support is disabled as per upstream request.
+	# readline is not really optional, bug #626504
+	# Does not build with Java 8
+	# Does not build with Python 3, bug #735238
+	econf \
+		--includedir="${EPREFIX}"/usr/include/libpisock \
+		--enable-conduits \
+		--with-readline \
+		$(use_enable threads) \
+		$(use_enable usb libusb) \
+		$(use_with png libpng) \
+		$(use_with bluetooth bluez) \
+		$(use_with perl) \
+		--without-java \
+		--without-tcl \
+		--without-python
+
+	if use perl; then
+		perl_set_version
+
+		cd bindings/Perl || die
+		perl-module_src_configure
+	fi
+}
+
+src_compile() {
+	emake
+
+	if use perl; then
+		cd bindings/Perl || die
+		local mymake=( OTHERLDFLAGS="${LDFLAGS} -L../../libpisock/.libs -lpisock" ) #308629
+		perl-module_src_compile
+	fi
+}
+
+src_install() {
+	default
+	dodoc doc/{README*,TODO}
+
+	if use perl; then
+		cd bindings/Perl || die
+		perl-module_src_install
+	fi
+
+	find "${ED}" -name '*.la' -delete || die
+}
diff --git a/app-text/xml2doc/files/xml2doc-20030510-c99.patch b/app-text/xml2doc/files/xml2doc-20030510-c99.patch
new file mode 100644
index 0000000000000..e38f703146d47
--- /dev/null
+++ b/app-text/xml2doc/files/xml2doc-20030510-c99.patch
@@ -0,0 +1,51 @@
+https://bugs.gentoo.org/923170
+--- a/src/defs.c
++++ b/src/defs.c
+@@ -1,5 +1,7 @@
+ #include "defs.h"
+ 
++#include <stdlib.h>
++
+ int defs_init()
+ {
+ 	DocS.page=0;
+--- a/src/defs.h
++++ b/src/defs.h
+@@ -1,6 +1,7 @@
+ #ifndef _INCLUDE_DEFS_H_
+ #define _INCLUDE_DEFS_H_
+ 
++#include <stdlib.h>
+ #include <stdio.h>
+ #include <string.h>
+ #include <unistd.h>
+--- a/src/main.c
++++ b/src/main.c
+@@ -1,5 +1,7 @@
+ #include "main.h"
+ 
++#include <stdlib.h>
++
+ /*
+  *
+  * PDF_set_value(p,"nameofvalue",(float)value); // get/set
+--- a/src/parse.c
++++ b/src/parse.c
+@@ -1,5 +1,7 @@
+ #include "defs.h"
+ 
++#include <stdlib.h>
++
+ int parse(const char *file)
+ {
+ 	Doc[n].doc=xmlParseFile(file);
+--- a/src/defs.c
++++ b/src/defs.c
+@@ -12,6 +12,7 @@ int defs_init()
+ 	DocS.add.colors=(struct_colors *)malloc(1);
+ 	DocS.add.pages =(struct_pages  *)malloc(1);
+ 	DocS.add.sizes =(struct_sizes  *)malloc(1);
++	return 0;
+ }
+ 
+ int defs_default() // Set default values
diff --git a/app-text/xml2doc/xml2doc-20030510-r2.ebuild b/app-text/xml2doc/xml2doc-20030510-r3.ebuild
similarity index 85%
rename from app-text/xml2doc/xml2doc-20030510-r2.ebuild
rename to app-text/xml2doc/xml2doc-20030510-r3.ebuild
index 85bbc1f14f7ea..96ee03405a29d 100644
--- a/app-text/xml2doc/xml2doc-20030510-r2.ebuild
+++ b/app-text/xml2doc/xml2doc-20030510-r3.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-inherit autotools toolchain-funcs
+inherit autotools flag-o-matic toolchain-funcs
 
 DESCRIPTION="Tool to convert simple XML to a variety of formats (pdf, html, txt, manpage)"
 HOMEPAGE="http://xml2doc.sourceforge.net"
@@ -24,6 +24,8 @@ PATCHES=(
 	"${FILESDIR}"/${P}-makefile.patch
 	# Fix GCC 10 -fno-common change
 	"${FILESDIR}"/${P}-gcc10-no-common.patch
+	# bug #923170
+	"${FILESDIR}"/${P}-c99.patch
 )
 
 src_prepare() {
@@ -35,6 +37,8 @@ src_prepare() {
 
 src_configure() {
 	tc-export CC
+	# bug #944764
+	append-cflags -std=gnu17
 	econf --disable-pdf
 }
 
diff --git a/dev-cpp/prometheus-cpp/prometheus-cpp-1.2.4.ebuild b/dev-cpp/prometheus-cpp/prometheus-cpp-1.2.4.ebuild
index 9c52336eeb1de..296f437914a35 100644
--- a/dev-cpp/prometheus-cpp/prometheus-cpp-1.2.4.ebuild
+++ b/dev-cpp/prometheus-cpp/prometheus-cpp-1.2.4.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://github.com/jupp0r/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~riscv x86"
+KEYWORDS="amd64 ~riscv x86"
 IUSE="test zlib"
 
 RESTRICT="!test? ( test )"
diff --git a/dev-ruby/json/json-2.10.2.ebuild b/dev-ruby/json/json-2.10.2.ebuild
index a5366b3fef2be..ff910ee58aeb6 100644
--- a/dev-ruby/json/json-2.10.2.ebuild
+++ b/dev-ruby/json/json-2.10.2.ebuild
@@ -20,7 +20,7 @@ SRC_URI="https://github.com/ruby/json/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 LICENSE="|| ( BSD-2 Ruby )"
 
 SLOT="$(ver_cut 1)"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~loong ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
+KEYWORDS="~alpha amd64 arm ~arm64 ~hppa ~loong ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc x86 ~amd64-linux ~x86-linux ~arm64-macos ~ppc-macos ~x64-macos ~x64-solaris"
 IUSE="doc test"
 
 DEPEND="dev-util/ragel"
diff --git a/dev-tex/rail/files/rail-1.2_p1-C23.patch b/dev-tex/rail/files/rail-1.2_p1-C23.patch
new file mode 100644
index 0000000000000..cdfc10264aae0
--- /dev/null
+++ b/dev-tex/rail/files/rail-1.2_p1-C23.patch
@@ -0,0 +1,359 @@
+Fix includes and function definitions and signatures
+until whole thing compiles with C23.
+https://bugs.gentoo.org/738854
+https://bugs.gentoo.org/883267
+https://bugs.gentoo.org/947155
+--- a/gram.y
++++ b/gram.y
+@@ -5,6 +5,7 @@
+ #include <stdio.h>
+ 
+ #include "rail.h"
++extern int yylex (void);
+ 
+ char optchar;
+ 
+--- a/rail.c
++++ b/rail.c
+@@ -21,6 +21,7 @@
+ #include <stdlib.h>
+ #include <stdio.h>
+ #include <string.h>
++#include <unistd.h>
+ 
+ #include "patchlevel.h"
+ #include "rail.h"
+@@ -54,9 +55,7 @@
+ 
+ int anonymous;		/* anonymous rules */
+ 
+-main(argc,argv)
+-unsigned argc;
+-char *argv[];
++int main(int argc, char *argv[])
+ {
+ 	char *arg, **argp;
+ 	unsigned len;
+@@ -122,8 +121,7 @@
+ 	/*NOTREACHED*/
+ }
+ 
+-int setopt(c,s)
+-char c, *s;
++int setopt(char c, char *s)
+ {
+ 	int set;
+ 
+@@ -167,7 +165,7 @@
+ 	return 1;
+ }
+ 
+-usage()
++void usage(void)
+ {
+ 	fprintf(stderr,USAGE,myname);
+ 	exit(1);
+@@ -175,23 +173,21 @@
+ 
+ /* error routine for yyparse() */
+ 
+-yyerror(s)
+-char *s;
++void yyerror(char *s)
+ {
+ 	fatal("%s",s);
+ }
+ 
+ /* wrap-up routine for yylex() */
+ 
+-yywrap()
++int yywrap(void)
+ {
+ 	return(1);
+ }
+ 
+ /* check for non-NULL pointer */
+ 
+-char *mcheck(s)
+-char *s;
++char *mcheck(char *s)
+ {
+ 	if(s==NULL)
+ 		fatal("out of memory",(char *)NULL);
+@@ -201,9 +197,7 @@
+ 
+ /* make a new body */
+ 
+-BODYTYPE *newbody(kind,body1,body2)
+-int kind;
+-BODYTYPE *body1, *body2;
++BODYTYPE *newbody(int kind, BODYTYPE *body1, BODYTYPE *body2)
+ {
+ 	BODYTYPE *body;
+ 
+@@ -226,8 +220,7 @@
+ 
+ /* free a body recursively */
+ 
+-freebody(body)
+-BODYTYPE *body;
++void freebody(BODYTYPE *body)
+ {
+ 	int i;
+ 
+@@ -246,16 +239,14 @@
+ 
+ /* test if a body is empty */
+ 
+-int isemptybody(body)
+-BODYTYPE *body;
++int isemptybody(BODYTYPE *body)
+ {
+ 	return(body==NULL || body->kind==EMPTY);
+ }
+ 
+ /* add to a body list */
+ 
+-static addlist(body1,body2)
+-BODYTYPE *body1, *body2;
++void static addlist(BODYTYPE *body1, BODYTYPE *body2)
+ {
+ 	if(body1->nlist>=MAXLIST) {
+ 		yyerror("list too long");
+@@ -265,9 +256,7 @@
+ 
+ /* add two body lists (for CAT, BAR, PLUS) */
+ 
+-BODYTYPE *addbody(kind,body1,body2)
+-int kind;
+-BODYTYPE *body1, *body2;
++BODYTYPE *addbody(int kind, BODYTYPE *body1, BODYTYPE *body2)
+ {
+ 	BODYTYPE *body;
+ 	int i;
+@@ -292,8 +281,7 @@
+ 
+ /* reverse all concatenations (for PLUS) */
+ 
+-BODYTYPE *revbody(body)
+-BODYTYPE *body;
++BODYTYPE *revbody(BODYTYPE *body)
+ {
+ 	int i,j;
+ 	BODYTYPE *tmp;
+@@ -314,9 +302,7 @@
+ 
+ /* print a body for debugging */
+ 
+-prtbody(indent,body)
+-int indent;
+-BODYTYPE *body;
++void prtbody(int indent, BODYTYPE *body)
+ {
+ 	int i;
+ 
+@@ -376,9 +362,7 @@
+ 
+ /* output a body */
+ 
+-outbody(id,body)
+-IDTYPE *id;
+-BODYTYPE *body;
++void outbody(IDTYPE *id, BODYTYPE *body)
+ {
+ 	posbody(body,0);
+ 
+@@ -403,10 +387,7 @@
+ 
+ /* format a body */
+ 
+-fmtbody(body,cent,arrow)
+-BODYTYPE *body;
+-char *cent;
+-char arrow;
++void fmtbody(BODYTYPE *body, char *cent, char arrow)
+ {
+ 	BODYTYPE *body1;
+ 	int i;
+@@ -494,8 +475,7 @@
+ 
+ /* position body (fill in height and ystart) */
+ 
+-posbody(body,ystart)
+-BODYTYPE *body;
++void posbody(BODYTYPE *body, int ystart)
+ {
+ 	BODYTYPE *body1;
+ 	int i;
+@@ -551,8 +531,7 @@
+ 
+ /* output an index entry */
+ 
+-outindex(id)
+-IDTYPE *id;
++int outindex(IDTYPE *id)
+ {
+ 	if(id!=NULL)
+ 		fprintf(outf,"\\rail@index{%s}\n",id->name);
+@@ -560,9 +539,7 @@
+ 
+ /* make a new rule list */
+ 
+-RULETYPE *newrule(id,body)
+-IDTYPE *id;
+-BODYTYPE *body;
++RULETYPE *newrule(IDTYPE *id, BODYTYPE *body)
+ {
+ 	RULETYPE *rule;
+ 
+@@ -576,8 +553,7 @@
+ 
+ /* free a rule list */
+ 
+-freerule(rule)
+-RULETYPE *rule;
++void freerule(RULETYPE *rule)
+ {
+ 	RULETYPE *rulep;
+ 
+@@ -591,8 +567,7 @@
+ 
+ /* add two rule lists */
+ 
+-RULETYPE *addrule(rule1,rule2)
+-RULETYPE *rule1, *rule2;
++RULETYPE *addrule(RULETYPE *rule1, RULETYPE *rule2)
+ {
+ 	RULETYPE *rulep;
+ 
+@@ -609,8 +584,7 @@
+ 
+ /* output a rule list */
+ 
+-outrule(rule)
+-RULETYPE *rule;
++void outrule(RULETYPE *rule)
+ {
+ 	while(rule!=NULL) {
+ 
+@@ -625,8 +599,7 @@
+ 
+ /* look up an identifier */
+ 
+-IDTYPE *lookup(name)
+-char *name;
++IDTYPE *lookup(char *name)
+ {
+ 	IDTYPE *idp, **idq;
+ 
+@@ -648,8 +621,7 @@
+ 
+ /* delete an identifier */
+ 
+-delete(id)
+-IDTYPE *id;
++void delete(IDTYPE *id)
+ {
+ 	IDTYPE *idp, **idq;
+ 
+@@ -665,7 +637,7 @@
+ 
+ /* check that there are no undefined identifiers */
+ 
+-checkdefs()
++void checkdefs(void)
+ {
+ 	IDTYPE *id;
+ 
+@@ -676,8 +648,7 @@
+ 
+ /* complain about an undefined identifier */
+ 
+-undef(id)
+-IDTYPE *id;
++void undef(IDTYPE *id)
+ {
+ 	if(chkgram)
+ 		error("undefined identifier '%s'",id->name);
+@@ -685,8 +656,7 @@
+ 
+ /* complain about a redefined identifier */
+ 
+-redef(id)
+-IDTYPE *id;
++void redef(IDTYPE *id)
+ {
+ 	if(chkgram)
+ 		error("redefined identifier '%s'",id->name);
+@@ -694,8 +664,7 @@
+ 
+ /* display an error */
+ 
+-error(f,s)
+-char *f, *s;
++void error(char *f, char *s)
+ {
+ 	if(newline) {
+ 		printf("\n");
+@@ -713,8 +682,7 @@
+ 	fprintf(stderr,"\n");
+ }
+ 
+-fatal(f,s)
+-char *f,*s;
++void fatal(char *f, char *s)
+ {
+ 	error(f,s);
+ 
+--- a/rail.h
++++ b/rail.h
+@@ -68,22 +68,31 @@
+ 
+ extern IDTYPE *errorid;
+ 
+-extern char *mcheck();
++extern char *mcheck(char *s);
+ 
+-extern BODYTYPE *newbody();
+-extern freebody();
+-extern int isemptybody();
+-extern BODYTYPE *addbody();
+-extern BODYTYPE *revbody();
+-
+-extern RULETYPE *newrule();
+-extern freerule();
+-extern RULETYPE *addrule();
+-extern outrule();
+-
+-extern IDTYPE *lookup();
+-extern delete();
+-
+-extern undef();
+-extern redef();
+-extern error();
++extern BODYTYPE *newbody(int kind, BODYTYPE *body1, BODYTYPE *body2);
++extern void freebody(BODYTYPE *body);
++extern int isemptybody(BODYTYPE *body);
++extern BODYTYPE *addbody(int kind, BODYTYPE *body1, BODYTYPE *body2);
++extern BODYTYPE *revbody(BODYTYPE *body);
++extern void posbody(BODYTYPE *body, int ystart);
++extern void fmtbody(BODYTYPE *body, char *cent, char arrow);
++
++extern RULETYPE *newrule(IDTYPE *id, BODYTYPE *body);
++extern void freerule(RULETYPE *rule);
++extern RULETYPE *addrule(RULETYPE *rule1, RULETYPE *rule2);
++extern void outrule(RULETYPE *rule);
++
++extern IDTYPE *lookup(char *name);
++extern void delete(IDTYPE *id);
++
++extern void undef(IDTYPE *id);
++extern void redef(IDTYPE *id);
++extern void error(char *f, char *s);
++extern void yyerror(char *s);
++extern int yywrap(void);
++
++int setopt(char c, char *s);
++void usage(void);
++void checkdefs(void);
++void fatal(char *f, char *s);
diff --git a/dev-tex/rail/files/rail-1.2_p1-makefile.patch b/dev-tex/rail/files/rail-1.2_p1-makefile.patch
new file mode 100644
index 0000000000000..44870b9a8c737
--- /dev/null
+++ b/dev-tex/rail/files/rail-1.2_p1-makefile.patch
@@ -0,0 +1,21 @@
+Correct Makefile, enabling parallel build.
+--- a/Makefile
++++ b/Makefile
+@@ -51,11 +53,15 @@
+ 
+ rail.o: patchlevel.h
+ 
++.PHONY: gram.c gram.h clean
++
+-gram.c gram.h: y.tab.c y.tab.h
++gram.c: y.tab.c
+ 	cmp -s gram.c y.tab.c || cp y.tab.c gram.c
++
++gram.h: y.tab.h
+ 	cmp -s gram.h y.tab.h || cp y.tab.h gram.h
+ 
+-y.tab.c y.tab.h y.output: gram.y
++y.tab.c y.tab.h y.output &: gram.y
+ 	$(YACC) $(YFLAGS) -dv gram.y
+ 
+ rail: $(OBJS)
diff --git a/dev-tex/rail/rail-1.2_p1-r1.ebuild b/dev-tex/rail/rail-1.2_p1-r2.ebuild
similarity index 83%
rename from dev-tex/rail/rail-1.2_p1-r1.ebuild
rename to dev-tex/rail/rail-1.2_p1-r2.ebuild
index cdd49433d9ca7..a11cd774b754a 100644
--- a/dev-tex/rail/rail-1.2_p1-r1.ebuild
+++ b/dev-tex/rail/rail-1.2_p1-r2.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit latex-package toolchain-funcs
 
@@ -18,8 +18,13 @@ BDEPEND="app-arch/unzip
 	app-alternatives/yacc
 	app-alternatives/lex"
 
+PATCHES=(
+	"${FILESDIR}/${P}-C23.patch"
+	"${FILESDIR}/${P}-makefile.patch"
+)
+
 src_compile() {
-	emake -j1 \
+	emake \
 		CC="$(tc-getCC)" \
 		CFLAGS="-DYYDEBUG ${CFLAGS} ${LDFLAGS}" \
 		rail rail.dvi
diff --git a/net-wireless/bss/bss-0.8-r3.ebuild b/net-wireless/bss/bss-0.8-r3.ebuild
new file mode 100644
index 0000000000000..436babb34ec3e
--- /dev/null
+++ b/net-wireless/bss/bss-0.8-r3.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Bluetooth stack smasher / fuzzer"
+HOMEPAGE="http://securitech.homeunix.org/blue/"
+SRC_URI="http://securitech.homeunix.org/blue/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+
+DEPEND="net-wireless/bluez"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-Makefile.patch
+	"${FILESDIR}"/${P}-includes.patch
+)
+
+src_configure() {
+	tc-export CC
+}
+
+src_install() {
+	dosbin bss
+	dodoc AUTHOR BUGS CHANGELOG CONTRIB NOTES README TODO \
+		replay_packet/replay_l2cap_packet.c
+}
diff --git a/net-wireless/bss/files/bss-0.8-Makefile.patch b/net-wireless/bss/files/bss-0.8-Makefile.patch
index 6238ea6ae9123..7f43808827321 100644
--- a/net-wireless/bss/files/bss-0.8-Makefile.patch
+++ b/net-wireless/bss/files/bss-0.8-Makefile.patch
@@ -1,3 +1,4 @@
+Make build system respect CFLAGS and PREFIX
 https://bugs.gentoo.org/725228
 --- a/Makefile
 +++ b/Makefile
@@ -25,7 +26,7 @@ https://bugs.gentoo.org/725228
 -	$(CC) -c $(L2P_SRC)
 -	$(CC) -c $(REP_SRC)
 -	$(CC) $(BSS_TMP) $(L2P_TMP) $(REP_TMP) -o $(BSS_OBJ) $(CFLAGS) $(BSS_FLAGS) $(BSS_LIBS)
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -c $(BSS_SRC) 
++	$(CC) $(CFLAGS) $(CPPFLAGS) -c $(BSS_SRC)
 +	$(CC) $(CFLAGS) $(CPPFLAGS) -c $(L2P_SRC)
 +	$(CC) $(CFLAGS) $(CPPFLAGS) -c $(REP_SRC)
 +	$(CC) $(LDFLAGS) $(BSS_TMP) $(L2P_TMP) $(REP_TMP) -o $(BSS_OBJ) $(CFLAGS) $(BSS_LIBS)
diff --git a/net-wireless/bss/files/bss-0.8-includes.patch b/net-wireless/bss/files/bss-0.8-includes.patch
new file mode 100644
index 0000000000000..e781484c34239
--- /dev/null
+++ b/net-wireless/bss/files/bss-0.8-includes.patch
@@ -0,0 +1,24 @@
+Add missing includes for compilation with C23
+https://bugs.gentoo.org/880799
+diff '--color=auto' -ru bss-0.8.old/bss.c bss-0.8/bss.c
+--- a/bss.c	2025-03-28 23:12:14.780857512 +0300
++++ b/bss.c	2025-03-28 23:13:44.003579006 +0300
+@@ -34,6 +34,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <stdlib.h>
++#include <time.h>
+ #include <unistd.h>
+ #include <sys/types.h>
+ #include <sys/socket.h>
+diff '--color=auto' -ru bss-0.8.old/replace.c bss-0.8/replace.c
+--- a/replace.c	2025-03-28 23:12:14.780857512 +0300
++++ b/replace.c	2025-03-28 23:14:07.107852000 +0300
+@@ -10,6 +10,7 @@
+ // Modifications by Ollie Whitehouse <ol at uncon dot org>
+ // 
+ #include <stdio.h>
++#include <string.h>
+ 
+ char *replace(char *string, char *oldpiece, char *newpiece) {
+ 
diff --git a/sci-biology/bamtools/bamtools-2.5.2-r1.ebuild b/sci-biology/bamtools/bamtools-2.5.2-r1.ebuild
new file mode 100644
index 0000000000000..d1d591465a0bd
--- /dev/null
+++ b/sci-biology/bamtools/bamtools-2.5.2-r1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake
+
+DESCRIPTION="A programmer's API and an end-user's toolkit for handling BAM files"
+HOMEPAGE="https://github.com/pezmaster31/bamtools"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/pezmaster31/bamtools.git"
+else
+	SRC_URI="https://github.com/pezmaster31/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0/${PV}" # no stable ABI yet
+
+RDEPEND="
+	>=dev-libs/jsoncpp-1.8.0:=
+	sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}"/"${P}-cmake.patch" )
+
+src_prepare() {
+	# delete bundled libs, just to be safe
+	rm -rf src/third_party/{gtest-1.6.0,jsoncpp} || die
+
+	cmake_src_prepare
+}
diff --git a/sci-biology/bamtools/bamtools-9999.ebuild b/sci-biology/bamtools/bamtools-9999.ebuild
index 78a0c3cd25533..7a9dd5b7532d9 100644
--- a/sci-biology/bamtools/bamtools-9999.ebuild
+++ b/sci-biology/bamtools/bamtools-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit cmake
 
diff --git a/sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch b/sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch
new file mode 100644
index 0000000000000..d67efeeb4f7b9
--- /dev/null
+++ b/sci-biology/bamtools/files/bamtools-2.5.2-cmake.patch
@@ -0,0 +1,26 @@
+Fix for CMake 4
+https://bugs.gentoo.org/951630
+https://github.com/pezmaster31/bamtools/commit/a610d2c0150d4b821aa4096e57eb77e4b0c14aa7
+From a610d2c0150d4b821aa4096e57eb77e4b0c14aa7 Mon Sep 17 00:00:00 2001
+From: David Seifert <SoapZA@users.noreply.github.com>
+Date: Sat, 31 Jul 2021 15:46:18 +0200
+Subject: [PATCH] CMakeLists.txt: CMake >= 3.11
+
+* `INCLUDE_GUARD_NAME` in `GENERATE_EXPORT_HEADER()` was added in 3.11
+
+Fixes: #216
+---
+ CMakeLists.txt | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index fc3a80c..2382802 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -1,4 +1,5 @@
+-cmake_minimum_required(VERSION 3.0)
++cmake_minimum_required(VERSION 3.11)
++# need 3.11 for INCLUDE_GUARD_NAME in GENERATE_EXPORT_HEADER
+ 
+ project(
+     BamTools
diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
index ef28f26e2b29f..58f8211e9ab99 100644
--- a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
+++ b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit toolchain-funcs
+inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Molecular dynamics simulations platform"
 HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html"
@@ -29,6 +29,9 @@ src_prepare() {
 }
 
 src_configure() {
+	# bug #944874
+	append-cflags -std=gnu17
+
 	#Individuals may want to edit the OPT* variables below.
 	#From the READ.ME:
 	#You may need to  "hand-tune" compiler or optimization options,