Merge branch 'release-4-5-patches'

diff --git a/admin/.cvsignore b/admin/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/admin/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/include/.cvsignore b/include/.cvsignore
deleted file mode 100644 (file)
index fd19000..0000000
--- a/include/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile.in
-Makefile
-config.h
-stamp-h.in

diff --git a/include/types/.cvsignore b/include/types/.cvsignore
deleted file mode 100644 (file)
index b840c21..0000000
--- a/include/types/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile.in
-Makefile
\ No newline at end of file

diff --git a/man/.cvsignore b/man/.cvsignore
deleted file mode 100644 (file)
index 3dda729..0000000
--- a/man/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile.in
-Makefile

diff --git a/man/man1/.cvsignore b/man/man1/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/man/man1/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/scripts/.cvsignore b/scripts/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/scripts/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/scripts/.gitignore b/scripts/.gitignore
new file mode 100644 (file)
index 0000000..a478607
--- /dev/null
+++ b/scripts/.gitignore
@@ -0,0 +1,2 @@
+GMXRC
+GMXRC.*

diff --git a/share/.cvsignore b/share/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/html/.cvsignore b/share/html/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/html/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/html/images/.cvsignore b/share/html/images/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/html/images/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/html/online/.cvsignore b/share/html/online/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/html/online/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/template/.cvsignore b/share/template/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/template/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/template/.gitignore b/share/template/.gitignore
new file mode 100644 (file)
index 0000000..5fda576
--- /dev/null
+++ b/share/template/.gitignore
@@ -0,0 +1,3 @@
+template
+gromacs
+Makefile.*-*

diff --git a/share/top/.cvsignore b/share/top/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/top/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/.cvsignore b/share/tutor/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/gmxdemo/.cvsignore b/share/tutor/gmxdemo/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/gmxdemo/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/methanol/.cvsignore b/share/tutor/methanol/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/methanol/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/mixed/.cvsignore b/share/tutor/mixed/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/mixed/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/nmr1/.cvsignore b/share/tutor/nmr1/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/nmr1/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/nmr2/.cvsignore b/share/tutor/nmr2/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/nmr2/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/speptide/.cvsignore b/share/tutor/speptide/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/speptide/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/share/tutor/water/.cvsignore b/share/tutor/water/.cvsignore
deleted file mode 100644 (file)
index 282522d..0000000
--- a/share/tutor/water/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-Makefile
-Makefile.in

diff --git a/src/.cvsignore b/src/.cvsignore
deleted file mode 100644 (file)
index 98a0226..0000000
--- a/src/.cvsignore
+++ /dev/null
@@ -1,6 +0,0 @@
-Makefile
-Makefile.in
-stamp-h.in
-stamp-h
-config.h
-config.h.in

diff --git a/src/contrib/.cvsignore b/src/contrib/.cvsignore
deleted file mode 100644 (file)
index eccc86b..0000000
--- a/src/contrib/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs
\ No newline at end of file

diff --git a/src/gmxlib/.cvsignore b/src/gmxlib/.cvsignore
deleted file mode 100644 (file)
index eccc86b..0000000
--- a/src/gmxlib/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs
\ No newline at end of file

diff --git a/src/gmxlib/selection/.cvsignore b/src/gmxlib/selection/.cvsignore
deleted file mode 100644 (file)
index 02b0523..0000000
--- a/src/gmxlib/selection/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs

diff --git a/src/gmxlib/trajana/.cvsignore b/src/gmxlib/trajana/.cvsignore
deleted file mode 100644 (file)
index e9407c9..0000000
--- a/src/gmxlib/trajana/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.libs
-.deps

diff --git a/src/kernel/.cvsignore b/src/kernel/.cvsignore
deleted file mode 100644 (file)
index eccc86b..0000000
--- a/src/kernel/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs
\ No newline at end of file

diff --git a/src/kernel/.gitignore b/src/kernel/.gitignore
index c8b084350e7b3971e61645f3434f15451f5b00e0..69ef8e7681b1890045a4939df9b74d75b5e3b735 100644 (file)
--- a/src/kernel/.gitignore
+++ b/src/kernel/.gitignore
@@ -1,2 +1,11 @@
 .deps
 .libs
+g_luck
+g_protonate
+g_x2top
+gmxcheck
+gmxdump
+grompp
+mdrun
+pdb2gmx
+tpbconv

diff --git a/src/mdlib/.cvsignore b/src/mdlib/.cvsignore
deleted file mode 100644 (file)
index eccc86b..0000000
--- a/src/mdlib/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs
\ No newline at end of file

diff --git a/src/ngmx/.cvsignore b/src/ngmx/.cvsignore
deleted file mode 100644 (file)
index eccc86b..0000000
--- a/src/ngmx/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs
\ No newline at end of file

diff --git a/src/ngmx/.gitignore b/src/ngmx/.gitignore
index c8b084350e7b3971e61645f3434f15451f5b00e0..4ee1e86940570d01dd27b0d07516df27a2d99c31 100644 (file)
--- a/src/ngmx/.gitignore
+++ b/src/ngmx/.gitignore
@@ -1,2 +1,6 @@
 .deps
 .libs
+g_highway
+g_logo
+g_xrama
+ngmx

diff --git a/src/tools/.cvsignore b/src/tools/.cvsignore
deleted file mode 100644 (file)
index eccc86b..0000000
--- a/src/tools/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-Makefile
-Makefile.in
-.deps
-.libs
\ No newline at end of file

diff --git a/src/tools/.gitignore b/src/tools/.gitignore
index c8b084350e7b3971e61645f3434f15451f5b00e0..5a69a3ab2700be30baa85dec48cf5d95b71023b3 100644 (file)
--- a/src/tools/.gitignore
+++ b/src/tools/.gitignore
@@ -1,2 +1,83 @@
 .deps
 .libs
+do_dssp
+editconf
+eneconv
+g_anadock
+g_anaeig
+g_analyze
+g_angle
+g_bar
+g_bond
+g_bundle
+g_chi
+g_cluster
+g_clustsize
+g_confrms
+g_covar
+g_current
+g_density
+g_densmap
+g_dielectric
+g_dih
+g_dipoles
+g_disre
+g_dist
+g_dyndom
+g_enemat
+g_energy
+g_filter
+g_gyrate
+g_h2order
+g_hbond
+g_helix
+g_helixorient
+g_kinetics
+g_lie
+g_mdmat
+g_membed
+g_mindist
+g_morph
+g_msd
+g_nmeig
+g_nmens
+g_nmtraj
+g_order
+g_polystat
+g_potential
+g_principal
+g_rama
+g_rdf
+g_rms
+g_rmsdist
+g_rmsf
+g_rotacf
+g_rotmat
+g_saltbr
+g_sas
+g_sdf
+g_select
+g_sgangle
+g_sham
+g_sigeps
+g_sorient
+g_spatial
+g_spol
+g_tcaf
+g_traj
+g_tune_pme
+g_vanhove
+g_velacc
+g_wham
+g_wheel
+genbox
+genconf
+genion
+genrestr
+make_edi
+make_ndx
+mk_angndx
+trjcat
+trjconv
+trjorder
+xpm2ps