This shall be a generic in-depth functionality guide to learn about mutt what it can do for you, from first steps to get things running up to the high end finetuning as seen in some configs of ConfigList & ConfigTricks.
A different approach is covered by the UseCases: how to reach a specific goal.

If you have specific requests as to Form, Structure, Style, Content, Topics, Items of the guide, then please have a look at the given items first to make sure it isn't provided yet. If it's still really lacking put it here between the lines as to-do...
Or just provide it yourself.

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to-do:

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Basics to get going

• MuttGuide/Introduction: How to use this guide.
• MailConcept: the way of mail between computers and inside yours.
• MuttGuide/Setup: compile-time, install, extra pkgs.
• MuttGuide/Syntax: run-time config file.
• MuttGuide/Folders: management, mbox, maildir, subfolders, shortcuts.

• MuttGuide/Actions (views, menus): modes, save, reply, forward, change folder, macros.
  • MuttGuide/Index?: display formats, colors, flags, errors.
  • MuttGuide/Message?: filter, charset, header weeding, colors.
  • MuttGuide/Attachment?: MIME for sending and reading, autoview.

• MuttGuide/Send: concept, compose, encoding.
  • MuttGuide/Headers: change From-ID, envelopes, alternates.
  • MuttGuide/Aliases: address management, external database.
  • MuttGuide/Edit?: pre-, post-processing, body, header

• MuttGuide/Receive: concept, spoolfile, mailboxes, notifications.
  • MuttGuide/Filesystem (local, NFS, permission, locking, mutt_dotlock.
  • MuttGuide/UsePOP: getting + processing, filter: fetchmail, procmail
  • MuttGuide/UseIMAP: remote folders.

Advanced stuff

• MuttGuide/Charsets? (what and why things can go wrong)
• Encryption (why, why not, security in stored files)
  • MuttGuide/UsePGP?
  • MuttGuide/UseGPG
  • MuttGuide/UseSMIME

• dynamic & complex configuration for special tasks
  • MuttGuide/Macros: save typing a lot same stuff
  • MuttGuide/Hooks: automatic actions.
  • MuttGuide/MailingLists?
  • MuttGuide/Scoring?
  • MuttGuide/Archiving

• MuttGuide/MultiAccounts: change profiles/ roles/ identities/ accounts/ From:-addresses.

Misc:

• general ConfigTricks.
• MuttGuide/XFace inclusion and display
• MuttGuide/Groups
• MuttGuide/Caching: Cache message headers (POP, IMAP, MH, Maildir) and bodies (POP, IMAP)

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If this guide didn't suit you, maybe one of the UseCases will.