I have now successfully set up mutt as my email client, but have three
issues remaining. They are listed below in order of increasing
seriousness.
  1) I have successfully set up macros for limiting the number of emails
I see, but would like to be able to have a default limiting expression
for when I first start mutt.
  2) I have placed all my emails in one maildir structure but would like
to back them up independently. I.e. 'cp'ing them only if the sender or
receiver had a particular address. This would have to be scriptable.
  3) I have set up several configuration files and made a maildir
structure but feel uncomfortable leaving my emails settings, e.g.
passwords, and messages in plain text files that anyone could read. I
have nothing to hide but feel this is insecure.
  To clarify the programs I have installed to manage my mail are: mutt
(obviously), getmail, procmail, and msmtp. I would very much appreciate
any help possible, as the last issue especially is a BIG problem.
 For the benefit of those reading this I will attach a copy of my .muttrc
rather than uploading it. Also for those wondering, explicitly setting my
from address to an empty string did not work as expected, instead mutt
very incorrectly guessed my address based on my login name and the name
of the computer I was working at. However this did not matter as by not
specifying a default account for msmtp I receive an error whenever
trying to send an email without explicitly setting the from address. 
  Finally a thank you in advance to anyone who can help :-).
# character set on messages that we send
set send_charset="utf-8"
# if there is no character set given on incoming messages, it is probably 
windows
set assumed_charset="iso-8859-1"

# make sure Vim knows mutt is a mail client and that we compose an UTF-8 
encoded message
set editor="vim -c 'set syntax=mail ft=mail enc=utf-8'"

# Tell mutt to use maildir format
set mbox_type=Maildir

# just scroll one line instead of full page
set menu_scroll=yes

# enable mailcap file
set mailcap_path=~/.mutt/mailcap

# we want to see some MIME types inline, see below this code listing for 
explanation
auto_view text/html
auto_view application/msword
auto_view application/pdf

# make default search pattern to search in To, Cc and Subject
set simple_search="~f %s | ~C %s | ~s %s"

# threading preferences, sort by threads
set sort=threads
set strict_threads=yes

# show spam score (from SpamAssassin only) when reading a message
spam "X-Spam-Score: ([0-9\\.]+).*" "SA: %1"
set pager_format = " %C - %[%H:%M] %.20v, %s%* %?H? [%H] ?"

# do not show all headers, just a few
ignore          *
unignore        From To Cc Bcc Date Subject
# and in this order
unhdr_order     *
hdr_order       From: To: Cc: Bcc: Date: Subject:

# brighten up stuff with colours, for more colouring examples see:
# http://aperiodic.net/phil/configs/mutt/colors
color normal      white          black
color hdrdefault  green          default
color quoted      green          default
color quoted1     yellow         default
color quoted2     red            default
color signature   cyan           default
color indicator   brightyellow   red
color error       brightred      default
color status      brightwhite    blue
color tree        brightmagenta  black
color tilde       blue           default
color attachment  brightyellow   default
color markers     brightred      default
color message     white          black
color search      brightwhite    magenta
color bold        brightyellow   default
# if you don't like the black progress bar at the bottom of the screen,
# comment out the following line
color progress    white          black

# spell-checking
set ispell="aspell -e -c"

# personality settings
set sendmail='/usr/bin/msmtp'
set reverse_name
set realname = "[CENSORED]"
unset from
set use_envelope_from
alternates "^[CENSORED]$"
alternates "^[CENSORED]$"
alternates "^[CENSORED]$"
alternates -group [CENSORED] "^[CENSORED]$" "^[CENSORED]$"
# this file must exist, and contains your signature, comment it out if
# you don't want a signature to be used
## set signature = ~/.signature

# aliases (sort of address book)
set alias_file=/data/mail/aliases
set sort_alias=alias
set reverse_alias=yes
source $alias_file

# account settings
set folder="/data/mail"
set spoolfile="+.Inbox"
set mask="!^\\.[^.]"
set record="+.Sent"
set postponed="+.Drafts"

# use headercache for IMAP (make sure this is a directory for performance!)
set header_cache=/tmp/.mutt

# mailboxes we want to monitor for new mail
  mailboxes ! `\
  for file in /data/mail/.*; do \
    box=$(basename "$file"); \
    if [ ! "$box" = '.' -a ! "$box" = '..' -a ! "$box" = '.customflags' \
      -a ! "$box" = '.subscriptions' ]; then \
      echo -n "\"+$box\" "; \
    fi; \
  done`
# mailboxes "="
# mailboxes "=Lists"

# mailing lists we are on (these are regexps!)
## subscribe "gentoo-.*@gentoo\\.org"

# Macros
macro index,pager c "<change-folder>?<toggle-mailboxes>" "open a different 
folder"
# macro pager c "<change-folder>?<toggle-mailboxes>" "open a different folder"
macro index,pager C "<copy-message>?<toggle-mailboxes>" "copy a message to a 
mailbox"
# macro index M "<save-message>?<toggle-mailboxes>" "move a message to a 
mailbox"
macro compose A "<attach-message>?<toggle-mailboxes>" "attach message(s) to 
this message"
# index limiting macros
macro index <F1> "<limit>~L [CENSORED]<enter>" "view email0" 
macro index <F2> "<limit>~L [CENSORED]<enter>" "view email1" 
macro index <F3> "<limit>~L [CENSORED]<enter>" "view email2" 
macro index <F4> "<limit>%L [CENSORED]<enter>" "view email group" 
macro index <F5> "<limit>~A<enter>" "view all emails"
# from address setting macros
macro compose <F1> "<edit-from><kill-line>[CENSORED] <[CENSORED]><enter>"
macro compose <F2> "<edit-from><kill-line>[CENSORED] <[CENSORED]><enter>"
macro compose <F3> "<edit-from><kill-line>[CENSORED] <[CENSORED]><enter>"
macro compose <F4> "<edit-from><kill-line>[CENSORED] <[CENSORED]><enter>"

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