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-What is the shell?

An interface for running programs and interacting with the OS and File System.
5 common shells: borne (sh), bourne-again (bash), korn (ksh), c-shell (csh), and tsch
default on Clear is tsch, default on sugar is bash (differences are mostly mini-language, such as setenv vs export for setting environment variable)

-Environment variables

they are simply variables that hold strings
these variables are inherited by programs run in the shell
to access the value of the environment variable in the shell, prepend the name with a $
the PATH variable tells the shell where to look for commands typed into the shell, ':' delimit different directories. We modify it so the hjc and hj commands can be found.
JAVA_HOME is needed so that the java compiler and jvm know where the needed libraries are located
HJ_HOME is set for the same reason but for the HJ compiler and subsystem
each shell inherits several environment variables on start, use the printenv command to see them

-Paths

absolute paths begin with '/' (called root, akin to C: )
relative paths don't have a starting '/' and are resolved relative to your current directory
'.' is a special directory name for the current directory
'..' is a special directory name for the parent directory
spaces need to be escaped by backslash or the whole path wrapped in quotes, otherwise the path is interpreted as separate arguments delimited by the spaces
tab will autocomplete directory or file names up to the first conflict

-Common Shell Commands

cd <dir> - change directory, takes a path
mv <src> <dest> - moves a file from src to dest, -R will move a folder
cp <src> <dest> - like move, but copies
ps - see current processes running, suspended, or terminated (but not yet harvested)
rm <fileOrDirName> - remove file, -R for directories. BE CAREFUL, there is no recovering what you delete. If you use the -f flag, rm will not ask confirmation about deleting each file. rm -Rf / will wipe the computer (hopefully you don't have permissions to do that)
mkdir <dirname> - creates a directory of the name given
chmod [args] <filename>- changes permissions
touch <filename> - changes modification and access times if the file already exists, creates a new file otherwise
ls - list contents of current directory
pwd - display path to working directory (current directory)
echo <string> - prints the string to the screen.
cat <filename> - prints the contents of file to the screen
grep <string> <filename> - prints the lines in file that contain the string
printenv - prints out all the environment variables and their values
man <cmdname> will display info regarding the specified command

-.Xrc Files

a shell script that is executed before the first shell prompt is presented to you
each shell has a .<shellname>rc file for itself, which is located in your home folder
ideal place to do setups (like setting up HJ_HOME, JAVA_HOME, and PATH) so they are always ready on start

-vim Text Editor

usage vim <filename> to open a file, without filename it reads from stdin
when you open a file with vim, you open it in command mode, which means your keys do something OTHER THAN TYPING THEIR VALUES, so don't do anything until you read the next bit.
the arrow keys move the cursor around
the keys h,j,k,l also move the cursor around
dd will delete the current line
a will change to append mode, and let you type after the cursor, press escape to exit append mode
i will change to insert mode, and let you type at the cursor, escape to exit
in command mode, you can type : for a few other commands and press enter to execute them
w will write your changes to your file without exiting vim
w <filename> will write to the specified file name overwriting it if it exists, or creating it if it doesn't.
q will quit if no changes haven't been saved.
q! will quit and discard unsaved changed.
typically to exit you'll use either :wq to save and quit, or :q! to discard your changes.
pressing escape will exit you out of colon commands
There are A TON of other commands to look up

-SSH and SFTP

ssh stands for Secure Shell
basically used for remote login
login format is %>ssh <username>@<address>
typical usage is <netid>@crystal.clear.rice.edu
you'll prompted for password then, just use your netID password (except for Sugar)
sftp stands for SSH File Transfer Protocol
typical commands are same as a shell, but are executed on the remote machine
prepend commands with an 'l' to execute on the local machine (ex. cd changes directory of remote machine, lcd changes local directory)
you cannot execute programs in sftp
%>put <src file> <dest file> copies the file from local to remote, renaming it if you specify a name different than the original
%>get <src file> <dest file> is put's inverse, copies from remote to local
the mput and mget variants will do their respective functions for multiple files.
Typically you'll specify a regular expression (well a subset anyway) instead of the file name.
%>mget * will get all files in the current directory of the remote machine.
%>mput *.hj will put all files ending in .hj in the local machine's current directory to the remote machine's current directory
quit, bye, or exit will log you out of ssh and sftp

-Signals

ctrl-C will interrupt the current running program, and get you back to the shell
ctrl-D sends EOF

-IO Redirection