Ubuntu 12.04 on a Toshiba Portégé R600

By 2012 my Ubuntu 9.04 was no longer supported so that I couldn't even install Chrome or such.  Updating was also no longer possible.  I still regarded my Portégé R600 as a much better daily companion than my former MacBook Pro.  Still amazed at its lightness and happy with its faultless heavy-duty high-productivity performance.  At the size and weight of the now-fashionable tablets, it was a full-fledged computer with full connectivity, excellent keyboard and screen, running everything I need identically to the large server I use too.  This made it desirable to renew its software.  I therefore did a clean install of Ubuntu 12.04, inspired by its LTS (long-term support) promise of at least five years not having to muck with my operating system.  Let me cite this Ubuntu forum again:
  Call me old fashioned, but I still don't see why I or anyone else 
  has to become an expert at saving this and that, tweak the other 
  and tweek the same, stand on your head and drink a pint of beer 
  from the far side of a glass, just so you can upgrade your 
  Ubuntu [...] without any problems.
  I just want to use my computer..... not program the damn thing!
It took me a week of googling to get Ubuntu 12.04 to work my way.  Eventually Gnome Classic gave me a similar 12-desktop 24-terminal environment as I had before.  With welcome improvements in addition to regaining support and updatability: automount for USB gadgets, better control of the noisy Portégé R600 fan, easier and better sound control, easier second-monitor projection, and more.

Installation detail (warning: this remains a snapshot anno June 2012):

Backup.   I started by backing up my whole 9.04 system on a new USB disk.  I formatted that with sudo mkfs -L BACKDISK /dev/sdb1 followed by sudo chown myusername:myusername /media/BACKDISK.  I wrote the backup with sudo rsync -vau --exclude /media/ / /media/BACKDISK/backup0904/, which is better than with cp -upr because it also copies the .xxx files and logical links.  It needs sudo for root-root etc ownership files.

Installation.   The initial install of Ubuntu 12.04 was problematic because my Portégé R600 wouldn't write an error-free boot CD-rom from the downloaded ubuntu-12.04-desktop-i386.iso file.  After too many endless installation tries I found that the check is that the CD should contain many folders, not just one large file.  I then tried to produce a boot USB stick using usb-creator found in my Ubuntu 9.04.  Apparently that was too old to produce a viable booter.  In the end, also in multiple tries, I wrote a working CD-rom on my discarded Mac (my wife has it) and installed Ubuntu 12.04 from that on my Portégé R600.  Font selection: English (US) with the Euro on 5 (with the ALT GR key to the right of the space bar).  I then installed my user directory with rsync -vau /media/BACKDISK/backup0904/home/myusername/ /home/.  And returned to the tcsh shell by adding tcsh at the end of ~/.bashrc and typing sudo chsh -s /usr/bin/tcsh.  Note: toshset no longer works but can be compiled back into the kernel following this recipe.  I did not because the fan noise and second monitor problems I had under Ubuntu 9.04 are solved in Ubuntu 12.04.

Desktop.   Ubuntu Unity was an unpleasant surprise.  Far too alike to macOS that had made me, in disgust, transfer to Ubuntu in 2009.  A too cluttered dock, too much mouse-clicking, as bad a workspace gadget as the Mac's (instead of the twelve clean desktops under the function keys that I am addicted to).  Fortunately, Gnome Classic [no specials effects] is at hand in Ubuntu 12.04 (sudo apt-get install gnome) and likely will be supported the coming years.  I installed it following this complete-concrete-concise instruction.  Style: Applications > System Tools > Preferences > Advanced settings > Theme.  For the window theme I like Metabox best but not its too loud Ubuntu-brown active-window title strip.  This theme collection furnished a Mint-theme.  Combining this under GTK+theme with Metabox under Window theme made the active-window title strip mint-green, perfect on my lightgreen background (get the menu by rightclicking with the cursor in the background; I prefer a smooth background).  Using this theme with emacs produced many Gtk warnings that went away with sudo apt-get install gtk2-engines-pixbuf following this thread.
Remaining bug: I get nested terminals that do not vanish at typing logout or exit.

Ubuntu packages.   Applications > Ubuntu Software Center > Edit > Ubuntu Software, turn on all types of software except source code.  Other Software: turn all on. Statistics: turn Submit on.  I installed (sudo apt-get install packagename): tcsh, csh, gnome, screen, xdotool, gconf-editor, emacs-23, emacs-goodies-el, auctex, gtk2-engines-pixbuf, texlive, texlive-lang-dutch, texlive-publishers, acroread, libreoffice, ap2s, paps, abiword, xfig, gv, mgdiff, xpdf, libjpeg62, gthumb, feh, qiv, gqview, mplayer2, ffmpeg, mencoder, transcode-utils, jhead, mutt, msmtp, elinks, fbreader, xine-ui, xine-plugin, lftp, libstdc++5, libxt-dev, dos2unix, adobe-flashplugin, mc, curl, youtube-dl, rar, gparted, disper, hfsprogs, ttf-inconsolata, git-core, tesseract-ocr, tesseract-ocr-eng, gpac, pdftk.

OpenOffice has become LibreOffice.  Adobe Reader (acroread) needs green light for website opening, defined under Edit > Preferences > Trust Manager > Change Settings.  Latex2html gave deprecation error messages that went away by commenting the offending lines out.  Xpdf gave segmentation faults; the remedy was to install an older version following Michael Gilbert's recipe after first installing libjpeg62.  Mplayer didn't play some .mov movies anymore; the remedy was to install mplayer2 instead with reinstall (sudo apt-get install --reinstall packagename) of ffmpeg and mencoder.

Other software.   Dropbox, Skype, Google Chrome, Google Earth, Calibre from their websites, usually downloading the xxx.deb into ~/Downloads and installing with sudo dpkg -i xxx.deb.  Chrome: in URL chrome://plugins/ disable /opt/google/chrome/PepperFlash/libpepflashplayer.so to get /usr/lib/adobe-flashplugin/libflashplayer.so.  IDL: not a (far too expensive) update but simply copying my old IDL 6.4 from my Ubuntu 9.04 backup with sudo rsync -vau /media/usb0/backup0904/usr/local/itt /usr/local/ including the license (opened by setenv LM_LICENSE_FILE /usr/local/itt/idl64/license.txt in ~/.cshrc).  The IDL help didn't work, which I repaired with sudo apt-get install libstdc++5,  adding this older version to Ubuntu's libstdc++6.  Viewer xv: again following this recipe plus installing libxt-dev and converter jpeg2ps.

Emacs.   Again a long day of trouble.  Why remains emacs so unpredictable and incomprehensible?  My workhorse emacs-snapshot-gtk was gone.  Color theme Feng Shui was not recognized.  Google delivered emacswiki, a warehouse of nerd stuff without useful information.  Finally, the answer found here is to add a line (color-theme-initialize) to file ~ /.emacs, not needed in Ubuntu 9.04.  For within-the-terminal sessions and my mutt-window mail answering I now need to use emacs -nw --color=no.  My special sessions now need --title windowname instead of the former -name windowname.  I keep my emacs windows clean with lines (tool-bar-mode -1)(menu-bar-mode -1)(scroll-bar-mode -1) in ~ /.emacs; CONTROL + rightclick delivers the menus when I need them.
Remaining bug: at session start the Emacs default windows flash distractingly and irritatingly into view before my specified layout comes up.

Cursor blink off.   Applications > System Tools > System settings > Keyboard.

Caps lock key to Compose key.   In Keyboard > Typing > Layout settings (left bottom) > Options (right bottom) > open Compose key position > flag Caps lock on.  Now you can type German: typing caps lock, ", and a gives ä.  Und so weiter.  This Wikipedia compose table specifies many more.

Panels.   For panel adaptations: ALT + rightclick on panel > Properties (this was rightclick without ALT in Ubuntu 9.04).  I have the panel bar with Applications, Places and notification area hidden at top right, a second panel bar with the workspace indicator and this-workspace window clickers hidden at bottom right.  No arrows on the un-hide clickers to minimize their width.
Remaining bug: the applet icons in the notification area do not resize with the panel width.

Workspaces.   I again have 12 labeled workspaces accessible with the function keys, defined in Applications > System Tools > System settings > Keyboard > Shortcuts > Navigation.  I set CNTRL + cursor left/right to shift one workspace left/right, and CNTRL + ALT + cursor left/right to shift the currently active window one workspace left/right.  I have two terminals in each workspace and perform specific tasks in each (like to-do, diary, and journal files under F1, mail under F11, browsing under F12).

Reboot.   With googled help I wrote script initworkspaces to auto-start my standard 12-workspace 30-session desktop layout at login. 

Mime defaults.   Define the defaults for the application that should open when clicking on linked files in .html or .pdf displays with mimeopen -d examplefile.typ.  This is a faster and better way than clicking on an example file of the given type in Places, for which the GUI does not offer command-line application specification anymore (it did in Ubuntu 9.04).  For example, to play movies in my talks I set them to click-start with a shell script calling mplayer -fs ${1} -loop 0 playing them full-screen in a loop without interruptions.  I click graphs and images into full-screen projection with feh -FZ which enables zoom-in with the mouse during a talk (depress the wheel and shift horizontally).

Browser.   I retrieved my Firefox profile and bookmarks from my Ubuntu 9.04 backup with sudo rsync -vau /media/usb0/backup0904/home/username/.mozilla ~/.  Google Chrome now installed properly (not in my Ubuntu 9.04) and appears to be a nice fast browser.  However, it does not play my .avi and .mov DOT movies and does not use my mime defaults.  No remedies found so far.

Second monitor / projector.   I followed Jon Dowland's Portégé recipe by getting to the BIOS (press ESC at startup), go to second page (Page Down), change setting "Power on display" to "LCD + Analog RGB".  I use alias alias vga-beamer 'xrandr --output LVDS1 --mode 1024x768 --output VGA1 --mode 1024x768 --same-as LVDS1' to start a talk projection, and alias alias vga-auto 'xrandr --output LVDS1 --auto --output VGA1 --auto' otherwise.  Another option is to use disper.
Remaining bug: a flat background (not wallpaper) becomes black and remains black.

Printing.   Selecting EN-US as language apparently sets the printing to letter size.  I use cups at http://localhost:631/ to manage printing: > Adding Printers and Classes > Add Printer. Then > Manage Printers, click on the printer name, > Administration > Set Default Options > media size A4 small margins, etc. I wake up cups with sudo service cups restart which seems to replace the former sudo /etc/init.d/cups restart, and I define the desired printer by specifying its name in ~ /.cups/lpoptions.  This way even the simple command lpr file works.

Update manager.   For some obscure reason the Ubuntu update notifier minimizes itself immediately on the workspace I happen to be on when it appears.  I added the window selector applet to the panel and click on it to find where it went and to reopen it.

Auto login / How to revive Ubuntu.   Because the Ubuntu updater often requires computer restart I tried to enable password-free automatic login so that I can do something else while it takes minutes to shut down and then again minutes to boot up and execute my desktop startup script, instead of having to pay attention and type my password halfway this lengthy procedure.  Oops: this became a nightmare.  My first try was sudo-editing /etc/lightdm/lightdm.conf as specified here.  It didn't work.  I then tried the GUI recipe: Applications > System Settings > User Accounts, unlock the lock at the top and slide the Automatic Login slider so that ON appears.  I relocked the lock.  Disaster: restarting my laptop gave a dark screen without any information or response.  Nothing, not even the grub booter.  I tried power-on pressing ESC, no success.  Deep-panic googling with my wife's Mac eventually gave me this excellent recipe.  Press SHIFT during power-on, select and boot the recovery-mode entry, cursor down to get the root shell prompt, type mount -o rw,remount / and you can do at least something.  I cleaned /etc/lightdm/lightdm.conf which didn't help.  Normal reboot then got stuck displaying text messages like "stopping system V runlevel compatibility".  Pressing CNTRL+ALT+F1 gave a command-line login.  Logging in to my user account and typing startx gave a Unity version of my Gnome startup script, with my aliases working but my scripts not working and with a weird low-resolution screen format.  Clicking on the gearwheel+spanner icon opened the settings GUI but the User Accounts GUI was locked and could not be unlocked.  I then went back to the recovery-mode boot and root command line, defined a root password with passwd -u root and passwd root, restarted with CNTRL+ALT+F1 login to the root account with the new root password.  Typing startx now gave a fresh default Unity opener screen.  The User Accounts GUI now had no lock.  Selecting my user account and shifting the Automatic Login slider back to the OFF position restored my laptop functionality.  Phew!  (In retrospect: typing sudo startx in the CNTRL+ALT+F1 user login might have worked without need for defining a root password which Ubuntu advises against.  I subsequently removed that and relocked the root account with sudo passwd -dl root on this advice).
Remaining bug: I guess I better live with having to type a password halfway the lengthy reboot.