proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

2 files changed, 58 insertions, 0 deletions

diff --git a/sci-biology/raxml/files/raxml-7.2.5-makefile.patch b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch
new file mode 100644
index 000000000000..8b381e50cb58
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.5-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 8d09549..59af556 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
++CC ?= gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE -fomit-frame-pointer -funroll-loops -O2 
++CFLAGS += -D_GNU_SOURCE
+ #-Wall -std=c99 -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport -pedantic-errors -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast
+ 
+ 
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
diff --git a/sci-biology/raxml/files/raxml-7.2.6-makefile.patch b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
new file mode 100644
index 000000000000..ae83e2eef4e7
--- /dev/null
+++ b/sci-biology/raxml/files/raxml-7.2.6-makefile.patch
@@ -0,0 +1,29 @@
+ Makefile.gcc |    6 +++---
+ 1 files changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/Makefile.gcc b/Makefile.gcc
+index 716b6c6..f0c1de2 100644
+--- a/Makefile.gcc
++++ b/Makefile.gcc
+@@ -1,10 +1,10 @@
+ # Makefile August 2006 by Alexandros Stamatakis
+ # Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>
+ 
+-CC = gcc 
++CC ?= gcc 
+ 
+ 
+-CFLAGS = -D_GNU_SOURCE  -fomit-frame-pointer -funroll-loops -O2 -msse
++CFLAGS += -D_GNU_SOURCE
+ 
+ 
+ 
+@@ -19,7 +19,7 @@ all : raxmlHPC
+ GLOBAL_DEPS = axml.h globalVariables.h
+ 
+ raxmlHPC : $(objs)
+-	$(CC) -o raxmlHPC $(objs) $(LIBRARIES) 
++	$(CC) $(LDFLAGS) -o raxmlHPC $(objs) $(LIBRARIES) 
+ 
+ classify.o : classify.c $(GLOBAL_DEPS)
+ evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)