Update README and manifest

README.md

@@ -18,7 +18,7 @@ There are two types of build for different purposes.
 This is the latest stable version. It is suitable for the most people for daily use.
 
 ```shell
-flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+flatpak remote-add --user --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
 flatpak install flathub io.github.pemsley.coot
 flatpak run io.github.pemsley.coot
 ```
@@ -28,7 +28,7 @@ flatpak run io.github.pemsley.coot
 **This isn’t meant to be the nightly build, but for the release that has some level of testing and is expected to mostly work and be usable to non-developer end-users.**
 
 ```shell
-flatpak remote-add --if-not-exists flathub-beta https://flathub.org/beta-repo/flathub-beta.flatpakrepo
+flatpak remote-add --user --if-not-exists flathub-beta https://flathub.org/beta-repo/flathub-beta.flatpakrepo
 flatpak install flathub-beta io.github.pemsley.coot
 flatpak run io.github.pemsley.coot//beta
 ```

io.github.pemsley.coot.yaml

@@ -101,7 +101,7 @@ modules:
         url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/libccp4-8.0.0.tar.gz
         sha256: cb813ae86612a0866329deab7cee96eac573d81be5b240341d40f9ad5322ff2d
 
-  - name: clipper4coot
+  - name: clipper
     buildsystem: autotools
     config-opts:
       - --enable-mmdb
@@ -118,7 +118,7 @@ modules:
         url: https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/clipper-2.1.20180802.tar.gz
         sha256: 7c7774f224b59458e0faa104d209da906c129523fa737e81eb3b99ec772b81e0
       - type: patch
-        path: clipper-configure-2.patch
+        path: patches/clipper-configure-2.patch
       - type: shell
         commands:
           - sed -i 's/libccp4c/ccp4c/g' configure
@@ -133,7 +133,7 @@ modules:
         url: https://github.com/libgd/libgd/releases/download/gd-2.3.3/libgd-2.3.3.tar.xz
         sha256: 3fe822ece20796060af63b7c60acb151e5844204d289da0ce08f8fdf131e5a61
       - type: patch
-        path: gd.h.patch
+        path: patches/gd.h.patch
 
   - name: raster3d
     buildsystem: simple
@@ -148,7 +148,7 @@ modules:
         url: http://www.bmsc.washington.edu/raster3d/Raster3D_3.0-7.tar.gz
         sha256: f566b499fee341db3a95229672c6afdbdb69da7faabdbe34f6e0d332d766160c
       - type: patch
-        path: Makefile.template.patch
+        path: patches/Makefile.template.patch
 
   - name: ssm
     buildsystem: autotools
@@ -345,7 +345,6 @@ modules:
         GLM_CFLAGS: "-I/app/include"
         GLM_LIBS: "-L/app/lib -lglm"
     post-install:
-      - mkdir -p ${FLATPAK_DEST}/share/coot/
       - cp -r python/ ${FLATPAK_DEST}/share/coot/
       - install -Dm644 pixmaps/icons/coot.svg ${FLATPAK_DEST}/share/icons/hicolor/scalable/apps/${FLATPAK_ID}.svg
       - install -Dm644 coot.desktop ${FLATPAK_DEST}/share/applications/${FLATPAK_ID}.desktop
@@ -355,4 +354,7 @@ modules:
       - type: git
         url: https://github.com/pemsley/coot.git
         tag: Release-1.1.18
-
+
+      # Refer to https://github.com/pemsley/coot/issues/161#issuecomment-3219446069
+      - type: patch
+        path: patches/Makefile.am.patch

patches/Makefile.am.patch

@@ -0,0 +1,36 @@
+diff --git a/Makefile.am b/Makefile.am
+index 94227b4b7..7e1c363f0 100644
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -1,18 +1,18 @@
+ # Makefile.am
+-# 
++#
+ # Copyright 2001, 2002, 2003, 2004, 2005, 2006, 2007 The University of York
+ # Author: Paul Emsley
+-# 
++#
+ # This program is free software; you can redistribute it and/or modify
+ # it under the terms of the GNU General Public License as published by
+ # the Free Software Foundation; either version 3 of the License, or (at
+ # your option) any later version.
+-# 
++#
+ # This program is distributed in the hope that it will be useful, but
+ # WITHOUT ANY WARRANTY; without even the implied warranty of
+ # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ # General Public License for more details.
+-# 
++#
+ # You should have received a copy of the GNU General Public License
+ # along with this program; if not, write to the Free Software
+ # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+@@ -45,7 +45,7 @@ else
+    SUBDIRS = auxil scheme python macros compat utils protein_db mini-mol geometry  \
+         lidia-core coot-utils angles ccp4mg-utils db-main analysis cootaneer ideal ligand coords \
+ 	density-contour skeleton high-res build MoleculesToTriangles pli greg-tests \
+-	python-tests cootilus fonts pyrogen data \
++	python-tests cootilus fonts pyrogen data monomers \
+ 	man rama-data doc glTF pixmaps textures sounds reference-structures api layla validation-graphs src ui
+ endif
+ endif