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Hi, here's my script to install Starflight 1 and 2 from GoG.
Nothing really special, except maybe that since they're DOS games, I'm using native dosbox instead of Windows dosbox. This has been tested to work with latest stable release of dosbox, 0.74, which actually is the same version as the Windows one.

A notice of warning, not related to this installer but to Starflight games: current savegame files are being modified as you play, so you cannot revert back to the state when you last saved by quitting the game without saving then restarting it: it would result in a corrupted savegame and you would not be able to continue.
To do this, you must keep around backups of your savegames (Starflight comes with a shell script wrapper to help you in this), and restore a previous copy. In this context "quitting without saving" makes sense to skip the time needed to make your current savegame consistent on disk when you know you're just about to restore a previous one over it.

Now the script:
https://raw.github.com/petchema/playonlinux/master/starflight1&2-gog

#!/bin/bash
# Date : (2011-12-01 22-38)
# Last revision : (2011-12-01 22-38)
# Wine version used : 
# Distribution used to test : Debian Sid (Unstable)
# Author : Pierre Etchemaite petchema@concept-micro.com
# Script licence : GPL v.2
# Program licence : Retail
# Depend : dosbox 

# prefer native dosbox version

[ -z "$PLAYONLINUX" ] && exit 0
source "$PLAYONLINUX/lib/sources"

abort () {
    POL_SetupWindow_message_image "$LNG_ABORTED" "$TITLE" "$PLAYONLINUX/themes/tango/warning.png"
    POL_SetupWindow_Close
    exit 1
}

check_install_archive () {
    POL_SetupWindow_wait_next_signal "$LNG_CHECK_ARCHIVE" "$TITLE"

    EXPECTED_NAME='setup_starflight_1_2.exe'
    EXPECTED_SIZE=44526203
    EXPECTED_MD5="4b3e884d1bbe066470338456991dc73e"

    # Temporarily prevent word splitting
    OLDIFS="$IFS"
    IFS=''
    NAME="$(basename $ARCHIVE)"
    SIZE="$(stat -c%s $ARCHIVE)"
    MD5="$(POL_MD5_file $ARCHIVE)"
    IFS="$OLDIFS"

    POL_SetupWindow_detect_exit

    if [ $SIZE -ne $EXPECTED_SIZE -o "$MD5" != "$EXPECTED_MD5" ]; then
        POL_SetupWindow_message_image "$LNG_ARCHIVE_MISMATCH\\nName: $NAME (expected $EXPECTED_NAME)\\nSize: $SIZE (expected $EXPECTED_SIZE)\\nMD5: $MD5\\n     (expected $EXPECTED_MD5)" "$TITLE" "$PLAYONLINUX/themes/tango/warning.png"
        POL_SetupWindow_question "$LNG_CONTINUE" "$TITLE"
        [ "$APP_ANSWER" != "TRUE" ] && abort
    fi
}


PREFIX="Starflight_1_2_gog"
WORKING_WINE_VERSION="1.3.23"
# GoG tools (graphic mode setup, code wheel work _almost_ ok with 1.3.23

case "$POL_LANG" in
    fr)
        TITLE="Starflight 1 et 2 (version GoG)"
        SHORTCUT1_NAME="Starflight 1"
        SHORTCUT1_CODEWHEEL="Starflight 1 - Roue de codes"
        SHORTCUT1_DOC="Starflight 1 - Manuel d'utilisation"
        SHORTCUT1_MAP="Starflight 1 - Carte stellaire"
        SHORTCUT2_NAME="Starflight 2"
        SHORTCUT2_DOC="Starflight 2 - Manuel d'utilisation"
        SHORTCUT2_MAP="Starflight 2 - Carte stellaire"
        LNG_ABORTED="Une erreur est survenue, l'installation est interrompue."
        LNG_CHECK_ARCHIVE="Test de l'archive d'installation..."
        LNG_ARCHIVE_MISMATCH="L'archive ne correspond pas.\\nOu bien elle est corrompue, ou ce n'est pas la version attendue.\\nCe script ne peut pas garantir que l'installation se passera bien, pensez à communiquer le résultat de l'installation sur le forum de PlayOnLinux."
	LNG_CONTINUE="Continuer ?"
        LNG_ARCHIVE_LOCATION="Indiquez l'emplacement de l'archive d'installation"
        LNG_SELECT_FILE="Sélectionnez le fichier"
        LNG_INSTALLING="Installation de $TITLE..."
        ;;
    *)
        TITLE="Starflight 1 and 2 (GoG release)"
        SHORTCUT1_NAME="Starflight 1"
        SHORTCUT1_CODEWHEEL="Starflight 1 - Code wheel"
        SHORTCUT1_DOC="Starflight 1 - User manual"
        SHORTCUT1_MAP="Starflight 1 - Stellar map"
        SHORTCUT2_NAME="Starflight 2"
        SHORTCUT2_DOC="Starflight 2 - User manual"
        SHORTCUT2_MAP="Starflight 2 - Stellar map"
        LNG_ABORTED="An error occurred, the installation is aborted."
        LNG_CHECK_ARCHIVE="Checking install archive..."
        LNG_ARCHIVE_MISMATCH="Install archive mismatch.\\nEither your install archive is corrupted, or is not the expected version.\\nThis script cannot guarantee that installation will work correctly. Please report success or failure to PlayOnLinux forums."
        LNG_CONTINUE="Continue?"
        LNG_ARCHIVE_LOCATION="Please select the location of the install file"
        LNG_SELECT_FILE="Select file"
        LNG_INSTALLING="Installing $TITLE..."
        ;;
esac

POL_SetupWindow_Init
POL_SetupWindow_presentation "$TITLE" "Binary Systems / Electronic Arts" "http://www.gog.com/en/gamecard/starflight_1_2" "Pierre Etchemaite" "$PREFIX"

check_one "dosbox" "dosbox"
POL_SetupWindow_missing
 
POL_Wine_SelectPrefix "$PREFIX"
POL_Wine_PrefixCreate

cd $HOME
POL_SetupWindow_browse "$LNG_ARCHIVE_LOCATION" "$LNG_SELECT_FILE"
ARCHIVE="$APP_ANSWER"

check_install_archive

if [ -n "$WORKING_WINE_VERSION" ]; then
    POL_Wine_InstallVersion "$WORKING_WINE_VERSION"
    export WINEVERSION="$WORKING_WINE_VERSION"
fi


POL_SetupWindow_wait_next_signal "$LNG_INSTALLING" "$TITLE"

# Associate .PDF with native app 
# http://wiki.winehq.org/FAQ#head-91bf3f0a8ccbfab8dee96f82fae2f1a489e0d243
# Do it before installing the game, so you have the possibility to open
# PDFs with Win32 reader if you choose to install it
cat <<'EOF' > $REPERTOIRE/tmp/pdfnativereader.reg
[HKEY_CLASSES_ROOT\\.pdf]
@="PDFfile"
"Content Type"="application/pdf"
[HKEY_CLASSES_ROOT\\PDFfile\\Shell\\Open\\command]
@="winebrowser \\"%1\\""
EOF
POL_Wine regedit $REPERTOIRE/tmp/pdfnativereader.reg

POL_Wine "$ARCHIVE" || abort

# GoG work!
Set_OS winxp


POL_SetupWindow_detect_exit

# Doesn't hurt ;)
POL_Wine_reboot 

# Sadly, it seems GoG installer unpacks both games even if you only ask for 1
# So test below is uneffective and all shortcuts are always created
if [ -d "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 1" ]; then
    # Better default settings in my opinion
    sed -i.orig -e 's/^fullscreen=.*/fullscreen=false/; s/^scaler=.*/scaler=hq2x/' "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 1/dosboxSF1.conf"

    POL_SetupWindow_make_shortcut "$PREFIX" "$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 1/" "C:/$PROGRAMFILES/GOG.com/Starflight 1 and 2/DOSBOX/DOSBox.exe" "-conf dosboxSF1.conf -noconsole" "$SHORTCUT1_NAME"
    cp -n "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 1/gfw_high.ico" "$REPERTOIRE/icones/32/$SHORTCUT1_NAME"
    # Thanks to exec, will only start W32 dosbox if native dosbox fails to start
    POL_Shortcut_InsertBeforeWine "$SHORTCUT1_NAME" "exec dosbox -conf dosboxSF1.conf"
    if [ -n "$WORKING_WINE_VERSION" ]; then
        Set_WineVersion_Assign "$WORKING_WINE_VERSION" "$SHORTCUT1_NAME"
    fi

    POL_Shortcut "Starflight_codes_by_gog.exe" "$SHORTCUT1_CODEWHEEL"

    POL_SetupWindow_make_shortcut "$PREFIX" "/windows/command" "start.exe" "" "$SHORTCUT1_DOC" "" "'C:/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 1/manual.pdf'"

    POL_SetupWindow_make_shortcut "$PREFIX" "/windows/command" "start.exe" "" "$SHORTCUT1_MAP" "" "'C:/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 1/map.pdf'"
fi

if [ -d "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 2" ]; then
    # Better default settings in my opinion
    sed -i.orig -e 's/^fullscreen=.*/fullscreen=false/; s/^scaler=.*/scaler=hq2x/' "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 2/dosboxSF2.conf"

    POL_SetupWindow_make_shortcut "$PREFIX" "$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 2/" "C:/$PROGRAMFILES/GOG.com/Starflight 1 and 2/DOSBOX/DOSBox.exe" "-conf dosboxSF2.conf -noconsole" "$SHORTCUT2_NAME"
    cp -n "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 2/gfw_high.ico" "$REPERTOIRE/icones/32/$SHORTCUT2_NAME"
    # Thanks to exec, will only start W32 dosbox if native dosbox fails to start
    POL_Shortcut_InsertBeforeWine "$SHORTCUT2_NAME" "exec dosbox -conf dosboxSF2.conf"
    if [ -n "$WORKING_WINE_VERSION" ]; then
        Set_WineVersion_Assign "$WORKING_WINE_VERSION" "$SHORTCUT2_NAME"
    fi

    POL_SetupWindow_make_shortcut "$PREFIX" "/windows/command" "start.exe" "" "$SHORTCUT2_DOC" "" "'C:/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 2/manual.pdf'"

    POL_SetupWindow_make_shortcut "$PREFIX" "/windows/command" "start.exe" "" "$SHORTCUT2_MAP" "" "'C:/$PROGRAMFILES/GOG.com/Starflight 1 and 2/Starflight 2/map.pdf'"
fi

POL_SetupWindow_Close

cat <<EOF > $REPERTOIRE/configurations/configurators/"$SHORTCUT1_NAME"
#!/bin/bash
[ -z "\\$PLAYONLINUX" ] && exit 0
source "\\$PLAYONLINUX/lib/sources"
export WINEPREFIX="$REPERTOIRE/wineprefix/$PREFIX"
export WINEDEBUG=""

POL_LoadVar_PROGRAMFILES

cd "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/" || exit

# Make sure that if user presses "start game", it will launch the right dosbox
DOSBOX="`which dosbox`"
if [ -n "\\$DOSBOX" ]; then
    cat <<-EOFINI > $REPERTOIRE/tmp/sf1nativedosbox.reg
	REGEDIT4

	[HKEY_LOCAL_MACHINE\\Software\\GOG.com\\GOGSTARFLIGHT1]
	"LAUNCHCOMMAND"="\\$DOSBOX -conf dosboxSF1.conf"
	EOFINI
    POL_Wine regedit $REPERTOIRE/tmp/sf1nativedosbox.reg
fi

POL_Wine "Graphic mode setup.exe" "GOGSTARFLIGHT1"
exit
EOF

cat <<EOF > $REPERTOIRE/configurations/configurators/"$SHORTCUT2_NAME"
#!/bin/bash
[ -z "\\$PLAYONLINUX" ] && exit 0
source "\\$PLAYONLINUX/lib/sources"
export WINEPREFIX="$REPERTOIRE/wineprefix/$PREFIX"
export WINEDEBUG=""

POL_LoadVar_PROGRAMFILES

cd "$WINEPREFIX/drive_c/$PROGRAMFILES/GOG.com/Starflight 1 and 2/" || exit
# Make sure that if user presses "start game", it will launch the right dosbox
DOSBOX="`which dosbox`"
if [ -n "\\$DOSBOX" ]; then
    cat <<-EOFINI > $REPERTOIRE/tmp/sf2nativedosbox.reg
	REGEDIT4

	[HKEY_LOCAL_MACHINE\\Software\\GOG.com\\GOGSTARFLIGHT2]
	"LAUNCHCOMMAND"="\\$DOSBOX -conf dosboxSF2.conf"
	EOFINI
    POL_Wine regedit $REPERTOIRE/tmp/sf2nativedosbox.reg
fi

POL_Wine "Graphic mode setup.exe" "GOGSTARFLIGHT2"
exit
EOF

exit

Edited by petch