use system-provided SQLite3 library

The reason is that we want to profit from latest security updates and
therefore not use a copy of the SQLite3 source code that becomes outdated.

ToDo: test on different Linux distributions / bc2 and adapt compile
instructions accordingly, also container recipes must be adapted.

CHANGELOG.txt

+Changes in Release 1.x.x
+--------------------------------------------------------------------------------
+
+ * Use system provided SQLite3 library
+
 Changes in Release 1.9.0
 --------------------------------------------------------------------------------
 

CMakeLists.txt

@@ -234,6 +234,7 @@ endif()
 
 find_package(Eigen 3.2.0 REQUIRED)
 find_package(Python 2.4 REQUIRED)
+find_package(SQLite3 REQUIRED)
 
 if(USE_NUMPY)
   find_package(Numpy REQUIRED)

cmake_support/FindSQLite3.cmake

+# Try to find SQLite3
+#
+# Once done this will define
+# - Find SQLite3
+# Find the native SQLite3 includes and library
+# 
+#  SQLITE3_INCLUDE_DIRS - SQLite3 include dirs.
+#  SQLITE3_LIBRARIES    - List of libraries when using SQLite3.
+#  SQLITE3_FOUND        - True if SQLite3 found.
+
+find_path(SQLITE3_INCLUDE_DIR NAMES sqlite3.h)
+find_library(SQLITE3_LIBRARY NAMES sqlite3)
+
+# handle the QUIETLY and REQUIRED arguments and set SQLITE3_FOUND to TRUE if 
+# all listed variables are TRUE
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
+IF(SQLITE3_FOUND)
+	SET(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})
+	SET(SQLITE3_LIBRARIES ${SQLITE3_LIBRARY})
+ELSE(SQLITE3_FOUND)
+	SET(SQLITE3_INCLUDE_DIRS)
+	SET(SQLITE3_LIBRARIES)
+ENDIF(SQLITE3_FOUND)
+
+mark_as_advanced(SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
+

modules/conop/src/compound_lib.hh

@@ -22,8 +22,7 @@
 #include <map>
 #include <boost/shared_ptr.hpp>
 
-// our own local copy of sqlite3
-#include <ost/db/sqlite3.h>
+#include <sqlite3.h>
 
 #include "module_config.hh"
 #include "compound.hh"

modules/db/src/CMakeLists.txt

 set(OST_DB_HEADERS
 sqlite_wrap.hh
-sqlite3.h
 sqlite_conv.hh
 module_config.hh
 )
 
 set(OST_DB_SOURCES
 sqlite_wrap.cc
-sqlite3.c
 )
 
 module(NAME db SOURCES ${OST_DB_SOURCES} HEADERS ${OST_DB_HEADERS} 
-       DEPENDS_ON ost_base)
+       DEPENDS_ON ost_base sqlite3)
 if(WIN32)
   set_target_properties(ost_db PROPERTIES LINK_FLAGS "/DEF:${CMAKE_CURRENT_SOURCE_DIR}/sqlite3.def")
   add_definitions(/DSQLITE_ENABLE_COLUMN_METADATA)

modules/db/src/sqlite_conv.hh

@@ -19,7 +19,7 @@
 #ifndef OST_IO_SQLITE_CONV_HH
 #define OST_IO_SQLITE_CONV_HH
 
-#include "sqlite3.h"
+#include <sqlite3.h>
 
 #include <ost/db/module_config.hh>
 

modules/db/src/sqlite_wrap.hh

@@ -29,7 +29,7 @@
 #include <ost/base.hh>
 #include <ost/message.hh>
 
-#include "sqlite3.h"
+#include <sqlite3.h>
 #include "sqlite_conv.hh"
 
 namespace ost { namespace db {

modules/doc/install.rst

@@ -33,6 +33,7 @@ required version is given in parentheses.
 * `Boost <http://boost.org>`_ (1.53)
 * `zlib <https://zlib.net/>`_ (usually comes with Boost or system)
 * `Eigen3 <http://eigen.tuxfamily.org>`_ (3.2.0)
+* `SQLite3 <https://www3.sqlite.org>`_ (3.7.13)`
 
 When you enable support for image processing, you will need:
 
@@ -215,6 +216,10 @@ can influence it.
     starting with `libtiff`)
   * `TIFF_INCLUDE_DIR` defines the include folder of libtiff (contains include
     files directly)
+  * `SQLITE3_LIBRARY` defines the location of the SQLite3 library (file name starting
+    with `libsqlite3`)
+  * `SQLITE3_INCLUDE_DIR` defines the include folder of SQLite3 (contains include
+    files directly)
   * Usually, you will receive errors for those variables when executing `cmake`
     and set them accordingly as needed.
 
@@ -300,7 +305,7 @@ All the dependencies can be installed from the package manager as follows:
 
   sudo apt-get install cmake sip-dev libtiff-dev libfftw3-dev libeigen3-dev \
                libpng-dev python-all python2.7 python-qt4 libboost-all-dev \
-               qt4-qtconfig qt4-qmake libqt4-dev libpng-dev
+               qt4-qtconfig qt4-qmake libqt4-dev libpng-dev libsqlite3-dev
 
 Now, all dependencies are located in standard locations and cmake will
 automatically find them without the need to pass any additional parameters. The