Merge pull request #3 from rranelli/master

Rename README to README.org

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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]].