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-# -*- mode: org -*-
-#+title: Bog
-#+options: toc:nil
-#+startup: showall
-
-Bog is a system for taking research notes in [[http://orgmode.org/][Org mode]]. It adds a few
-research-specific features, nearly all of which are focused on managing
-and taking notes with Org, not on writing research articles with Org.
-
-* Installation
-
-Bog is available on [[http://melpa.milkbox.net/][MELPA]].
-
-To enable Bog in all Org buffers, add it to =org-mode-hook=.
-
-#+begin_src emacs-lisp
-  (add-hook 'org-mode-hook 'bog-mode)
-#+end_src
-
-* Workflow
-
-The Bog workflow is focused around the citekey, which is the only study
-information that must be included in the notes. This unique identifier
-is used as a link to the BibTeX file and other associated files.
-
-In the example below, the citekey "name2000word" is a study heading. A
-study heading is defined as a heading the has a citekey as a title or as
-the value of =bog-citekey-property=. When a citekey occurs anywhere else
-(like "another1999study" below), they are taken as a reference to
-another study (which may or may not have a subtree in this or another
-Org file).
-
-#+begin_example
-
-  ,* Topic heading
-
-  ,** TODO name2000word                               :atag:
-
-  <URL for study>
-
-  Article notes ... a reference to another1999study ...
-#+end_example
-
-The default format for the citekey is the first author's last name, the
-year, and then the first non-trivial word. To have BibTeX mode
-automatically generate a key of this format, the =bibtex-autokey-*=
-settings can be modified.
-
-#+begin_src emacs-lisp
-  (setq bibtex-autokey-year-length 4
-        bibtex-autokey-titleword-length nil
-        bibtex-autokey-titlewords-stretch 0
-        bibtex-autokey-titlewords 1
-        bibtex-autokey-year-title-separator "")
-#+end_src
-
-* Main features
-
-Many Bog functions take the citekey from the notes. If the point is on a
-citekey (like "another1999study" above), then that citekey will be used.
-If this fails, many functions will try to take the citekey from the
-first parent heading that is a study heading.
-
-- =bog-find-citekey-file=
-
-  Open an associated file (usually a PDF) for a citekey.
-
-- =bog-find-citekey-bib=
-
-  Open a BibTeX file for a citekey.
-
-  BibTeX entries can be stored in one of two ways:
-  - As a single file with many entries
-  - As single-entry files named citekey.bib within a common directory
-
-- =bog-search-citekey-on-web=
-
-  Search Google Scholar for a citekey. The default citekey format (first
-  author's last name, year, and first non-trivial word) usually contains
-  enough information to make this search successful.
-
-- =bog-rename-staged-file-to-citekey=
-
-  Rename a new file (usually a PDF) to be associated with a citekey.
-
-- =bog-clean-and-rename-staged-bibs=
-
-  Rename new BibTeX files. If a separate BibTeX file is used for each
-  citekey, this function can be used to rename all new BibTeX files.
-  =bibtex-clean-entry= is used to clean the entry and autogenerate the
-  key.
-
-- =bog-create-combined-bib=
-
-  Generate a combined BibTeX file for all citekeys in buffer. This is
-  useful if single-entry BibTeX files are used.
-
-Other useful functions include
-
-- =bog-goto-citekey-heading-in-buffer=
-- =bog-goto-citekey-heading-in-notes=
-- =bog-citekey-tree-to-indirect-buffer=
-- =bog-refile=
-- =bog-search-notes=
-- =bog-search-notes-for-citekey=
-- =bog-sort-topic-headings-in-buffer=
-- =bog-sort-topic-headings-in-notes=
-- =bog-insert-heading-citekey=
-- =bog-open-first-citekey-link=
-
-* Variables
-
-Several variables determine where Bog looks for things.
-
-- =bog-notes-directory=
-- =bog-file-directory=
-- =bog-bib-directory= or =bog-bib-file=
-- =bog-stage-directory=
-
-The variables below are important for specifying how Bog behaves.
-
-- =bog-citekey-format=
-
-  A regular expression that defines the format used for citekeys
-
-- =bog-find-citekey-bib-function=
-
-  A function to find a citekey in a BibTeX file. This determines whether
-  a directory of single-entry BibTeX files or a single BibTeX file is
-  used.
-
-* Keybindings
-
-A keymap is defined for Bog under the prefix =C-c "​=. If you prefer
-something else (like =C-c b=), set =bog-keymap-prefix=.
-
-Some Bog functions are useful outside of an Org buffer (e.g.,
-=bog-search-notes=). These functions are available through the
-=bog-commander= interface (based of off =projectile-commander=). This
-can be bound to a global key for quick access.
-
-* Other approaches
-
-If Bog doesn't fit your workflow, there are a good number of other
-approaches to explore. On the Org mode mailing list, there are some [[http://thread.gmane.org/gmane.emacs.orgmode/78983][nice]]
-[[http://thread.gmane.org/gmane.emacs.orgmode/14756][descriptions]] of systems people have come up with for taking research
-notes in Org. For a package that focuses on both taking research notes
-and writing research articles, look into [[https://github.com/jkitchin/jmax/blob/master/org/org-ref.org][Org-ref]].