Merge pull request #3 from rranelli/master

Rename README to README.org

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-Bog is a system for taking research notes in [Org mode](http://orgmode.org/). 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 [MELPA](http://melpa.milkbox.net/).
-
-To enable Bog in all Org buffers, add it to `org-mode-hook`.
-
-    (add-hook 'org-mode-hook 'bog-mode)
-
-# 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).
-
-    * Topic heading
-    
-    ** TODO name2000word                               :atag:
-    
-    <URL for study>
-    
-    Article notes ... a reference to another1999study ...
-
-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.
-
-    (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 "")
-
-# 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 [nice](http://thread.gmane.org/gmane.emacs.orgmode/78983)
-[descriptions](http://thread.gmane.org/gmane.emacs.orgmode/14756) 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 [Org-ref](https://github.com/jkitchin/jmax/blob/master/org/org-ref.org).
\ No newline at end of file