#----------------------------------*-sh-*--------------------------------------
# =========                 |
# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
#  \\    /   O peration     | Website:  https://openfoam.org
#   \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
#    \\/     M anipulation  |
#------------------------------------------------------------------------------
# License
#     This file is part of OpenFOAM.
#
#     OpenFOAM 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.
#
#     OpenFOAM 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 OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
#
# File
#     etc/bashrc
#
# Description
#     Startup file for OpenFOAM
#     Sourced from ~/.profile or ~/.bashrc
#     Should be usable by any POSIX-compliant shell (eg, ksh)
#
#------------------------------------------------------------------------------

export WM_PROJECT=OpenFOAM
export WM_PROJECT_VERSION=dev

################################################################################
# USER EDITABLE PART: Changes made here may be lost with the next upgrade
#
# FOAM_INST_DIR is the location of the OpenFOAM installation which defaults to
# the directory containing this file if sourced by a bash shell.
#
# Please set to the appropriate path if the default is not correct.
#
[ "$BASH" -o "$ZSH_NAME" ] && \
export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
export FOAM_INST_DIR=$HOME/$WM_PROJECT
# export FOAM_INST_DIR=~$WM_PROJECT
# export FOAM_INST_DIR=/opt/$WM_PROJECT
# export FOAM_INST_DIR=/usr/local/$WM_PROJECT
#
# END OF (NORMAL) USER EDITABLE PART
################################################################################

# The default environment variables below can be overridden in a prefs.sh file
# located in ~/.OpenFOAM/$WM_PROJECT_VERSION, ~/.OpenFOAM,
# $FOAM_INST_DIR/site/$WM_PROJECT_VERSION or $FOAM_INST_DIR/site

#- Compiler location:
#    WM_COMPILER_TYPE= system | ThirdParty (OpenFOAM)
export WM_COMPILER_TYPE=system

#- Compiler:
#    WM_COMPILER = Gcc | Gcc48 ... Gcc62 | Clang | Icc
export WM_COMPILER=Gcc
unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH

#- Memory addressing:
#    On a 64bit OS this can be 32bit or 64bit
#    On a 32bit OS addressing is 32bit and this option is not used
#    WM_ARCH_OPTION = 32 | 64
export WM_ARCH_OPTION=64

#- Precision:
#    WM_PRECISION_OPTION = SP | DP | LP
export WM_PRECISION_OPTION=DP

#- Label size:
#    WM_LABEL_SIZE = 32 | 64
export WM_LABEL_SIZE=32

#- Optimised, debug, profiling:
#    WM_COMPILE_OPTION = Opt | Debug | Prof
export WM_COMPILE_OPTION=Opt

#- MPI implementation:
#    WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI
#               | MPI | FJMPI | QSMPI | SGIMPI | INTELMPI
export WM_MPLIB=SYSTEMOPENMPI

#- Operating System:
#    WM_OSTYPE = POSIX | ???
export WM_OSTYPE=POSIX

#- Floating-point signal handling:
#    set or unset
export FOAM_SIGFPE=

#- memory initialisation:
#    set or unset
#export FOAM_SETNAN=


################################################################################

# The old dirs to be cleaned from the environment variables
foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
    $HOME/$WM_PROJECT/$USER $FOAM_USER_APPBIN $FOAM_USER_LIBBIN \
    $WM_PROJECT_SITE $FOAM_SITE_APPBIN $FOAM_SITE_LIBBIN"

# Location of installation
# ~~~~~~~~~~~~~~~~~~~~~~~~
export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION

WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ]
then
    export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL
fi
unset WM_PROJECT_DIR_REAL

# Location of third-party software
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION

WM_THIRD_PARTY_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc" ]
then
    export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL
fi
unset WM_THIRD_PARTY_DIR_REAL

# Location of site-specific templates etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# unset is equivalent to $WM_PROJECT_INST_DIR/site
if [ -d "$WM_PROJECT_SITE" ]
then
    export WM_PROJECT_SITE
else
    unset WM_PROJECT_SITE
fi

# Location of user files
# ~~~~~~~~~~~~~~~~~~~~~~
export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION

# Source initialization functions
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
. $WM_PROJECT_DIR/etc/config.sh/functions

# Add in preset user or site preferences:
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`

# Evaluate command-line parameters and record settings for later
# these can be used to set/unset values, or specify alternative pref files
export FOAM_SETTINGS="$@"
_foamEval $@

# Clean standard environment variables (PATH, LD_LIBRARY_PATH, MANPATH)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
foamClean=$WM_PROJECT_DIR/bin/foamCleanPath

#- Clean PATH
cleaned=`$foamClean "$PATH" "$foamOldDirs"` && PATH="$cleaned"

#- Clean LD_LIBRARY_PATH
cleaned=`$foamClean "$LD_LIBRARY_PATH" "$foamOldDirs"` \
    && LD_LIBRARY_PATH="$cleaned"

#- Clean MANPATH
cleaned=`$foamClean "$MANPATH" "$foamOldDirs"` && MANPATH="$cleaned"

export PATH LD_LIBRARY_PATH MANPATH


# Source project setup files
# ~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamSource $WM_PROJECT_DIR/etc/config.sh/settings
_foamSource $WM_PROJECT_DIR/etc/config.sh/aliases


# Source user setup files for optional packages
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi`
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/paraview`
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/ensight`
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/gperftools`

if [ ! -z "$FOAMY_HEX_MESH" ]
then
    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/CGAL`
fi


# Clean environment paths again. Only remove duplicates
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#- Clean PATH
cleaned=`$foamClean "$PATH"` && PATH="$cleaned"

#- Clean LD_LIBRARY_PATH
cleaned=`$foamClean "$LD_LIBRARY_PATH"` && LD_LIBRARY_PATH="$cleaned"

#- Clean MANPATH (trailing ':' to find system pages)
cleaned=`$foamClean "$MANPATH"`: && MANPATH="$cleaned"

export PATH LD_LIBRARY_PATH MANPATH

#- Clean LD_PRELOAD
if [ -n "$LD_PRELOAD" ]
then
    cleaned=`$foamClean "$LD_PRELOAD"` && LD_PRELOAD="$cleaned"
    export LD_PRELOAD
fi


# Cleanup environment:
# ~~~~~~~~~~~~~~~~~~~~
unset cleaned foamClean foamOldDirs


# Unload initialization functions:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
. $WM_PROJECT_DIR/etc/config.sh/functions

# Source the bash completion file:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ "$BASH" ] && . $WM_PROJECT_DIR/etc/config.sh/bash_completion

#------------------------------------------------------------------------------

diff --git a/etc/bashrc b/etc/bashrc
index ae19940..f55914a 100644
--- a/etc/bashrc
+++ b/etc/bashrc
@@ -113,10 +113,24 @@ foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
 export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
 export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
 
+WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
+if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ]
+then
+    export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL
+fi
+unset WM_PROJECT_DIR_REAL
+
 # Location of third-party software
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
 
+WM_THIRD_PARTY_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
+if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc" ]
+then
+    export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL
+fi
+unset WM_THIRD_PARTY_DIR_REAL
+
 # Location of site-specific templates etc
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # unset is equivalent to $WM_PROJECT_INST_DIR/site

#----------------------------------*-sh-*--------------------------------------
# =========                 |
# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
#  \\    /   O peration     | Website:  https://openfoam.org
#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
#    \\/     M anipulation  |
#------------------------------------------------------------------------------
# License
#     This file is part of OpenFOAM.
#
#     OpenFOAM 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.
#
#     OpenFOAM 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 OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
#
# File
#     etc/bashrc
#
# Description
#     Startup file for OpenFOAM
#     Sourced from ~/.profile or ~/.bashrc
#     Should be usable by any POSIX-compliant shell (eg, ksh)
#
#------------------------------------------------------------------------------

export WM_PROJECT=OpenFOAM
export WM_PROJECT_VERSION=dev

################################################################################
# USER EDITABLE PART: Changes made here may be lost with the next upgrade
#
# FOAM_INST_DIR is the location of the OpenFOAM installation which defaults to
# the directory containing this file if sourced by a bash shell.
#
# Please set to the appropriate path if the default is not correct.
#
[ "$BASH" -o "$ZSH_NAME" ] && \
export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
export FOAM_INST_DIR=$HOME/$WM_PROJECT
# export FOAM_INST_DIR=~$WM_PROJECT
# export FOAM_INST_DIR=/opt/$WM_PROJECT
# export FOAM_INST_DIR=/usr/local/$WM_PROJECT
#
# END OF (NORMAL) USER EDITABLE PART
################################################################################

# The default environment variables below can be overridden in a prefs.sh file
# located in ~/.OpenFOAM/$WM_PROJECT_VERSION, ~/.OpenFOAM,
# $FOAM_INST_DIR/site/$WM_PROJECT_VERSION or $FOAM_INST_DIR/site

#- Compiler location:
#    WM_COMPILER_TYPE= system | ThirdParty (OpenFOAM)
export WM_COMPILER_TYPE=system

#- Compiler:
#    WM_COMPILER = Gcc | Gcc48 ... Gcc62 | Clang | Icc
export WM_COMPILER=Gcc
unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH

#- Memory addressing:
#    On a 64bit OS this can be 32bit or 64bit
#    On a 32bit OS addressing is 32bit and this option is not used
#    WM_ARCH_OPTION = 32 | 64
export WM_ARCH_OPTION=64

#- Precision:
#    WM_PRECISION_OPTION = SP | DP | LP
export WM_PRECISION_OPTION=DP

#- Label size:
#    WM_LABEL_SIZE = 32 | 64
export WM_LABEL_SIZE=32

#- Optimised, debug, profiling:
#    WM_COMPILE_OPTION = Opt | Debug | Prof
export WM_COMPILE_OPTION=Opt

#- MPI implementation:
#    WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI
#               | MPI | FJMPI | QSMPI | SGIMPI | INTELMPI
export WM_MPLIB=SYSTEMOPENMPI

#- Operating System:
#    WM_OSTYPE = POSIX | ???
export WM_OSTYPE=POSIX

#- Floating-point signal handling:
#    set or unset
export FOAM_SIGFPE=

#- memory initialisation:
#    set or unset
#export FOAM_SETNAN=


################################################################################

# The old dirs to be cleaned from the environment variables
foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
    $HOME/$WM_PROJECT/$USER $FOAM_USER_APPBIN $FOAM_USER_LIBBIN \
    $WM_PROJECT_SITE $FOAM_SITE_APPBIN $FOAM_SITE_LIBBIN"

# Location of installation
# ~~~~~~~~~~~~~~~~~~~~~~~~
export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION

if [ -d "$WM_PROJECT_DIR" ]
then
    WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
    if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ]
    then
        export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL
    fi
    unset WM_PROJECT_DIR_REAL
fi

# Location of third-party software
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION

if [ -d "$WM_THIRD_PARTY_DIR" ]
then
    WM_THIRD_PARTY_DIR_REAL=$(cd $WM_THIRD_PARTY_DIR && pwd -P)
    if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc/tools" ]
    then
        export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL
    fi
    unset WM_THIRD_PARTY_DIR_REAL
fi

# Location of site-specific templates etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# unset is equivalent to $WM_PROJECT_INST_DIR/site
if [ -d "$WM_PROJECT_SITE" ]
then
    export WM_PROJECT_SITE
else
    unset WM_PROJECT_SITE
fi

# Location of user files
# ~~~~~~~~~~~~~~~~~~~~~~
export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION

# Source initialization functions
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
. $WM_PROJECT_DIR/etc/config.sh/functions

# Add in preset user or site preferences:
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`

# Evaluate command-line parameters and record settings for later
# these can be used to set/unset values, or specify alternative pref files
export FOAM_SETTINGS="$@"
_foamEval $@

# Clean standard environment variables (PATH, LD_LIBRARY_PATH, MANPATH)
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
foamClean=$WM_PROJECT_DIR/bin/foamCleanPath

#- Clean PATH
cleaned=`$foamClean "$PATH" "$foamOldDirs"` && PATH="$cleaned"

#- Clean LD_LIBRARY_PATH
cleaned=`$foamClean "$LD_LIBRARY_PATH" "$foamOldDirs"` \
    && LD_LIBRARY_PATH="$cleaned"

#- Clean MANPATH
cleaned=`$foamClean "$MANPATH" "$foamOldDirs"` && MANPATH="$cleaned"

export PATH LD_LIBRARY_PATH MANPATH


# Source project setup files
# ~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamSource $WM_PROJECT_DIR/etc/config.sh/settings
_foamSource $WM_PROJECT_DIR/etc/config.sh/aliases


# Source user setup files for optional packages
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi`
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/paraview`
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/ensight`
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/gperftools`

if [ ! -z "$FOAMY_HEX_MESH" ]
then
    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/CGAL`
fi


# Clean environment paths again. Only remove duplicates
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#- Clean PATH
cleaned=`$foamClean "$PATH"` && PATH="$cleaned"

#- Clean LD_LIBRARY_PATH
cleaned=`$foamClean "$LD_LIBRARY_PATH"` && LD_LIBRARY_PATH="$cleaned"

#- Clean MANPATH (trailing ':' to find system pages)
cleaned=`$foamClean "$MANPATH"`: && MANPATH="$cleaned"

export PATH LD_LIBRARY_PATH MANPATH

#- Clean LD_PRELOAD
if [ -n "$LD_PRELOAD" ]
then
    cleaned=`$foamClean "$LD_PRELOAD"` && LD_PRELOAD="$cleaned"
    export LD_PRELOAD
fi


# Cleanup environment:
# ~~~~~~~~~~~~~~~~~~~~
unset cleaned foamClean foamOldDirs


# Unload initialization functions:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
. $WM_PROJECT_DIR/etc/config.sh/functions

# Source the bash completion file:
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ "$BASH" ] && . $WM_PROJECT_DIR/etc/config.sh/bash_completion

#------------------------------------------------------------------------------

diff --git a/etc/bashrc b/etc/bashrc
index ae19940..5f5d9d9 100644
--- a/etc/bashrc
+++ b/etc/bashrc
@@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     | Website:  https://openfoam.org
-#   \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -113,10 +113,30 @@ foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
 export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
 export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
 
+if [ -d "$WM_PROJECT_DIR" ]
+then
+    WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
+    if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ]
+    then
+        export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL
+    fi
+    unset WM_PROJECT_DIR_REAL
+fi
+
 # Location of third-party software
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
 
+if [ -d "$WM_THIRD_PARTY_DIR" ]
+then
+    WM_THIRD_PARTY_DIR_REAL=$(cd $WM_THIRD_PARTY_DIR && pwd -P)
+    if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc/tools" ]
+    then
+        export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL
+    fi
+    unset WM_THIRD_PARTY_DIR_REAL
+fi
+
 # Location of site-specific templates etc
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # unset is equivalent to $WM_PROJECT_INST_DIR/site

diff --git a/etc/bashrc b/etc/bashrc
index ae19940..5f5d9d9 100644
--- a/etc/bashrc
+++ b/etc/bashrc
@@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     | Website:  https://openfoam.org
-#   \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -113,10 +113,30 @@ foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
 export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
 export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
 
+if [ -d "$WM_PROJECT_DIR" ]
+then
+    WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
+    if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ]
+    then
+        export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL
+    fi
+    unset WM_PROJECT_DIR_REAL
+fi
+
 # Location of third-party software
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
 
+if [ -d "$WM_THIRD_PARTY_DIR" ]
+then
+    WM_THIRD_PARTY_DIR_REAL=$(cd $WM_THIRD_PARTY_DIR && pwd -P)
+    if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc/tools" ]
+    then
+        export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL
+    fi
+    unset WM_THIRD_PARTY_DIR_REAL
+fi
+
 # Location of site-specific templates etc
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # unset is equivalent to $WM_PROJECT_INST_DIR/site
diff --git a/wmake/wclean b/wmake/wclean
index 8ccd637..3c3d80d 100755
--- a/wmake/wclean
+++ b/wmake/wclean
@@ -3,7 +3,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     | Website:  https://openfoam.org
-#   \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -260,10 +260,11 @@ unset targetType
 if [ -d "$MakeDir" ]
 then
     objectsDir=$MakeDir/$WM_OPTIONS
-    if [[ "$PWD" = *"$WM_PROJECT_DIR"* ]]
+    expandPath "$PWD"
+    if [[ "$exPath" = *"$WM_PROJECT_DIR"* ]]
     then
         platformPath=$WM_PROJECT_DIR/platforms/${WM_OPTIONS}
-        objectsDir=$platformPath${PWD//$WM_PROJECT_DIR/}
+        objectsDir=$platformPath${exPath//$WM_PROJECT_DIR/}
     fi
     rm -rf "$objectsDir" 2>/dev/null
 fi

#!/bin/bash
#------------------------------------------------------------------------------
# =========                 |
# \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
#  \\    /   O peration     | Website:  https://openfoam.org
#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
#    \\/     M anipulation  |
#------------------------------------------------------------------------------
# License
#     This file is part of OpenFOAM.
#
#     OpenFOAM 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.
#
#     OpenFOAM 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 OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
#
# Script
#     wclean
#
# Usage
#     wclean [OPTION] [dir]
#     wclean [OPTION] target [dir [MakeDir]]
#
# Description
#     Clean up the wmake control directory Make/\$WM_OPTIONS and remove the
#     lnInclude directories generated for libraries.
#
#------------------------------------------------------------------------------
Script=${0##*/}

# Source the wmake functions
# shellcheck source=scripts/wmakeFunctions
. "${0%/*}/scripts/wmakeFunctions"

error() {
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
    usage
    exit 1
}

usage() {
    cat<<USAGE

Usage: $Script [OPTION] [dir]
       $Script [OPTION] target [dir [MakeDir]]

options:
  -silent | -s      Ignored - for compatibility with wmake
  -help             Print the usage

Clean up the wmake control directory Make/\$WM_OPTIONS and remove the
lnInclude directories generated for libraries.

The targets correspond to a subset of the 'wmake' special targets:
  all               All subdirectories, uses any Allwclean or Allclean
                    files if they exist
  exe | lib | libo | libso
                    Clean Make, any *.dep files and lnInclude directories
  empty             Remove empty sub-directories for the requested dir.
                    If executed in the main project directory, it will also
                    remove deprecated object directories and respective binaries
                    that refer to no-longer-existing source code.

USAGE
}


#------------------------------------------------------------------------------
# Parse arguments and options
#------------------------------------------------------------------------------

while [ "$#" -gt 0 ]
do
    case "$1" in
    -h | -help)
        usage && exit 0
        ;;
    -s | -silent)    # Ignored - for compatibility with wmake
        shift
        ;;
    -*)
        error "unknown option: '$*'"
        ;;
    *)
        break
        ;;
    esac
done


#------------------------------------------------------------------------------
# Check arguments and change to the directory in which to run wclean
#------------------------------------------------------------------------------

unset dir targetType
MakeDir=Make

if [ $# -ge 1 ]
then

    if [ -d "$1" ]
    then
        dir=$1
    else
        targetType=$1
    fi

    # Specified directory name:
    [ $# -ge 2 ] && dir=$2

    # Specified alternative name for the Make sub-directory:
    [ $# -ge 3 ] && MakeDir=$3

    if [ "$dir" ]
    then
        cd "$dir" 2>/dev/null || {
            echo "$Script error: could not change to directory '$dir'" 1>&2
            exit 1
        }
    fi

    # Print command
    [ -z "$targetType" ] || targetSpace=" "
    echo "$Script $targetType$targetSpace${dir:-.}"
fi


#------------------------------------------------------------------------------
# If target not specified search up the directory tree for the Make
# sub-directory, check the existence of the 'files' file and clean there if
# present
# ------------------------------------------------------------------------------

[ -n "$targetType" ] || cdSource


#------------------------------------------------------------------------------
# Remove empty sub-directories and exit
#------------------------------------------------------------------------------

if [ "$targetType" = empty ]
then
    # First pass: clean up empty source code directories

    echo "Removing empty directories..."

    # Get sub-directories avoiding particular directories
    # shellcheck disable=SC2044
    for dir in $(find . -mindepth 1 -maxdepth 1 \
                        -type d \( -name .git -prune -o -print \) )
    do
        echo "    searching: $dir"
        find "$dir" -depth -type d -empty -exec rmdir {} \; -print
    done

    # Second pass: clean up object directories with WM_PROJECT_DIR that don't
    # have respective source code folders, along with the respective binaries

    expandPath "$PWD"
    if [ "$exPath" = "$WM_PROJECT_DIR" ]
    then
        findObjectDir "$PWD"

        if [ -d "$objectsDir" ]
        then
            echo "    Removing redundant object directories in $objectsDir"

            find "$objectsDir" -name 'variables' -print | \
            while read -r variablesFile
            do
                # Hack'ish way of getting the original source code path
                depFile=$(dirname "$variablesFile")
                depToSource "$depFile"

                # Check if the original source code directory exists
                if [ ! -r "$sourceFile" ]
                then
                    # Delete the respective binary first
                    binaryFile=$(grep -e '^ *\(EXE\|LIB\) *= *' "$variablesFile")

                    # Catch all file extension (o,a,so,?+) for libraries
                    if echo "$binaryFile" | grep -qe '^ *LIB *= *'
                    then
                        binaryFile="${binaryFile}.*"
                    fi

                    # Isolate path and translate environment variables
                    binaryFile=$(echo "$binaryFile" | \
                                 sed -e 's/^ *\(EXE\|LIB\) *= *//' \
                                     -e 's/(/{/g' -e 's/)/}/g' )

                    # Expand environment variables for path
                    binaryFile=$(eval echo "$binaryFile")

                    # Verbosely remove binary file
                    if [ -n "$binaryFile" ] && [ -e "$binaryFile" ]
                    then
                        rm -vf "$binaryFile" 2>/dev/null
                    fi

                    # Remove the deprecated object directory
                    rm -rvf "$depFile" 2>/dev/null
                fi
            done
        fi
    fi

    exit 0
fi


#------------------------------------------------------------------------------
# Recurse the directories tree
#------------------------------------------------------------------------------

if [ "$targetType" = all ]
then
    if [ -e Allwclean ]       # Consistent with Allwmake
    then
        ./Allwclean
        exit $?
    elif [ -e Allclean ]      # Often used for tutorial cases
    then
        ./Allclean
        exit $?
    else
        # For all the sub-directories containing a 'Make' directory
        # shellcheck disable=SC2044
        for dir in $(find . \( -type d -a -name Make \))
        do
            dir=${dir%/Make} # Parent directory - trim /Make from the end

            # If Allwclean exists execute otherwise wclean
            if [ -e "$dir/Allwclean" ]
            then
                "$dir/Allwclean"
            else
                $0 "$dir"
            fi
        done
    fi
fi

# targetType is not needed beyond this point
unset targetType


#------------------------------------------------------------------------------
# Clean the 'Make' directory if present
#------------------------------------------------------------------------------

if [ -d "$MakeDir" ]
then
    objectsDir=$MakeDir/$WM_OPTIONS
    expandPath "$PWD"
    if [[ "$exPath" = *"$WM_PROJECT_DIR"* ]]
    then
        platformPath=$WM_PROJECT_DIR/platforms/${WM_OPTIONS}
        objectsDir=$platformPath${exPath//$WM_PROJECT_DIR/}
    fi
    rm -rf "$objectsDir" 2>/dev/null
fi


#------------------------------------------------------------------------------
# Remove the lnInclude directory if present
#------------------------------------------------------------------------------

if [ -d lnInclude ]
then
    rm -rf lnInclude 2>/dev/null
fi


#------------------------------------------------------------------------------
# Cleanup local variables and functions
#------------------------------------------------------------------------------

unset Script usage error MakeDir


#------------------------------------------------------------------------------

diff --git a/etc/bashrc b/etc/bashrc
index ae19940..5f5d9d9 100644
--- a/etc/bashrc
+++ b/etc/bashrc
@@ -2,7 +2,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     | Website:  https://openfoam.org
-#   \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -113,10 +113,30 @@ foamOldDirs="$WM_PROJECT_DIR $WM_THIRD_PARTY_DIR \
 export WM_PROJECT_INST_DIR=$FOAM_INST_DIR
 export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION
 
+if [ -d "$WM_PROJECT_DIR" ]
+then
+    WM_PROJECT_DIR_REAL=$(cd $WM_PROJECT_DIR && pwd -P)
+    if [ -d "$WM_PROJECT_DIR_REAL" -a -e "$WM_PROJECT_DIR_REAL/etc/bashrc" ]
+    then
+        export WM_PROJECT_DIR=$WM_PROJECT_DIR_REAL
+    fi
+    unset WM_PROJECT_DIR_REAL
+fi
+
 # Location of third-party software
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION
 
+if [ -d "$WM_THIRD_PARTY_DIR" ]
+then
+    WM_THIRD_PARTY_DIR_REAL=$(cd $WM_THIRD_PARTY_DIR && pwd -P)
+    if [ -d "$WM_THIRD_PARTY_DIR_REAL" -a -e "$WM_THIRD_PARTY_DIR_REAL/etc/tools" ]
+    then
+        export WM_THIRD_PARTY_DIR=$WM_THIRD_PARTY_DIR_REAL
+    fi
+    unset WM_THIRD_PARTY_DIR_REAL
+fi
+
 # Location of site-specific templates etc
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # unset is equivalent to $WM_PROJECT_INST_DIR/site
diff --git a/wmake/wclean b/wmake/wclean
index 8ccd637..3c3d80d 100755
--- a/wmake/wclean
+++ b/wmake/wclean
@@ -3,7 +3,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     | Website:  https://openfoam.org
-#   \\  /    A nd           | Copyright (C) 2011-2018 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2011-2019 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -260,10 +260,11 @@ unset targetType
 if [ -d "$MakeDir" ]
 then
     objectsDir=$MakeDir/$WM_OPTIONS
-    if [[ "$PWD" = *"$WM_PROJECT_DIR"* ]]
+    expandPath "$PWD"
+    if [[ "$exPath" = *"$WM_PROJECT_DIR"* ]]
     then
         platformPath=$WM_PROJECT_DIR/platforms/${WM_OPTIONS}
-        objectsDir=$platformPath${PWD//$WM_PROJECT_DIR/}
+        objectsDir=$platformPath${exPath//$WM_PROJECT_DIR/}
     fi
     rm -rf "$objectsDir" 2>/dev/null
 fi
diff --git a/wmake/wrmdep b/wmake/wrmdep
index 1999b25..2cb138a 100755
--- a/wmake/wrmdep
+++ b/wmake/wrmdep
@@ -3,7 +3,7 @@
 # =========                 |
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     | Website:  https://openfoam.org
-#   \\  /    A nd           | Copyright (C) 2015-2018 OpenFOAM Foundation
+#   \\  /    A nd           | Copyright (C) 2015-2019 OpenFOAM Foundation
 #    \\/     M anipulation  |
 #------------------------------------------------------------------------------
 # License
@@ -227,12 +227,16 @@ oldFolders)
 
 updateMode)
 
-    if [ "$PWD" != "$WM_PROJECT_DIR" ]
+    expandPath "$PWD"
+    if [ "$exPath" != "$WM_PROJECT_DIR" ]
     then
         echo "Cannot 'update', not in the project top-level directory"
         exit 1
     fi
 
+    # Go into the real path
+    cd "$exPath"
+
     echo "Removing dep files corresponding to source files that no longer exist..."
     fileNameList=$(find -L src applications -name '*.[CHL]' -type l)