Added the tools.rst file (still a stub) and did some heavy editing of…

… the README. Also added to Code of Conduct.

README.md

@@ -1,6 +1,6 @@
 # README #
 
-This repository links to the Tilia Manual/FAQ and provides a link to the [Tilia software](http://www.tiliait.com/).
+This repository links to the [Tilia Manual](http://tilia-manual.readthedocs.org) which support the [Tilia software](http://www.tiliait.com/).
 
 Author:
 =======
@@ -9,6 +9,22 @@ Neotoma Development Team
 
 This work is funded through support to the Neotoma Project through NSF Geosciences (award number pending).
 
+We welcome contributions from any individual, whether code, documentation, or issue tracking. All participants are expected to follow the [code of conduct](http://github.com/SimonGoring/tilia-manual/code_of_conduct.md) for this project.
+
 License:
 ========
-The original documentation herein is licensed under an MIT license.  This Documentation makes use of [Sphinx](http://www.sphinx-doc.org/en/stable/) and ReStructuredText.  Sphinx is licensed under a BSD license.  The [Shinx RTD Theme](https://github.com/snide/sphinx_rtd_theme) is licensed under an MIT License.
+The original documentation herein is licensed under an MIT license.  This Documentation makes use of [Sphinx](http://www.sphinx-doc.org/en/stable/) and ReStructuredText.  Sphinx is licensed under a BSD license.
+
+Development
+==========
+The manual is scripted using plain-text files with [ReStructuredText](http://docutils.sourceforge.net/docs/user/rst/quickstart.html) markdown all saved in the `docs` folder (with an `rst` extension).  [readthedocs](http://readthedocs.org) uses a workflow where documents generated in `rst` files are then compiled to `HTML` using a Python parser called Sphinx to generate the documentation.  Once the file is compiled it is then pushed up to the GitHub repository (you're here now) and is then cloned & re-compiled by readthedocs, where it becomes available at [](http://tilia-manual.readthedocs.org)
+
+Currently the files within the manual are structured (somewhat) hierarchically:
+
+* `index.rst` : The header for the documentation.  Compiles [here](http://tilia-manual.readthedocs.org/en/latest/index.html).  Contains the Acknowledgements and the Table of Contents.  Acts as a simple homepage for the Manual.
+* `get_tilia.rst` : Downloading & Installation instructions for Tilia. Compiles [here](http://tilia-manual.readthedocs.org/en/latest/get_tilia.html)
+* `creating` : How to create a new Tilia file. Compiles [here](http://tilia-manual.readthedocs.org/en/latest/creating.html)
+* `overview.rst` : Presumes that a file has been generated. An overview of an empty Tilia file.  Compiles [here](http://tilia-manual.readthedocs.org/en/latest/overview.html)
+* `edit_data.rst` : How to go about editing a Tilia file.  Both practical and best-practices.  Compiles [here](http://tilia-manual.readthedocs.org/en/latest/edit_data.html)
+* `tools.rst` : Still a stub.  This is intended to present the various features of Tilia that aren't part of the core editing process. Compiles [here](http://tilia-manual.readthedocs.org/en/latest/tools.html)
+* `steward.rst` : Proposed but not developed.

code_of_conduct.md

@@ -0,0 +1,50 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of
+  fostering an open and welcoming community, we pledge to respect all people who
+  contribute through reporting issues, posting feature requests, updating
+  documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+  experience for everyone, regardless of level of experience, gender, gender
+    identity and expression, sexual orientation, disability, personal appearance,
+    body size, race, ethnicity, age, religion, or nationality.
+
+  Examples of unacceptable behavior by participants include:
+
+    * The use of sexualized language or imagery
+    * Personal attacks
+    * Trolling or insulting/derogatory comments
+    * Public or private harassment
+    * Publishing other's private information, such as physical or electronic
+    addresses, without explicit permission
+    * Other unethical or unprofessional conduct
+
+    Project maintainers have the right and responsibility to remove, edit, or
+    reject comments, commits, code, wiki edits, issues, and other contributions
+    that are not aligned to this Code of Conduct, or to ban temporarily or
+    permanently any contributor for other behaviors that they deem inappropriate,
+    threatening, offensive, or harmful.
+
+    By adopting this Code of Conduct, project maintainers commit themselves to
+      fairly and consistently applying these principles to every aspect of managing
+      this project. Project maintainers who do not follow or enforce the Code of
+        Conduct may be permanently removed from the project team.
+
+      This Code of Conduct applies both within project spaces and in public spaces
+        when an individual is representing the project or its community.
+
+      Instances of abusive, harassing, or otherwise unacceptable behavior may be
+        reported by contacting a project maintainer at [INSERT EMAIL ADDRESS]. All
+        complaints will be reviewed and investigated and will result in a response that
+        is deemed necessary and appropriate to the circumstances. Maintainers are
+        obligated to maintain confidentiality with regard to the reporter of an
+        incident.
+
+
+      This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+                                                                     version 1.3.0, available at
+        [http://contributor-covenant.org/version/1/3/0/][version]
+
+        [homepage]: http://contributor-covenant.org
+        [version]: http://contributor-covenant.org/version/1/3/0/

docs/_build/html/_sources/creating.txt

@@ -1,4 +1,4 @@
-Creating a New Tilia File:
+Creating a New Tilia File
 ========================================
 
 Open up the Tilia program and open a new file (**File** > **New**).  A new window will open up, with two tabs at the top (Data & Metadata), several columns (Code, Name and Group) and a single header cell, by default **Pollen**.
@@ -9,3 +9,18 @@ Open up the Tilia program and open a new file (**File** > **New**).  A new windo
    A brand new empty data file.
 
 The cell that contains the term **Pollen** can be modified to represent one of the other dataset types that Neotoma supports.  Once you have selected the dataset type, it’s possible to then load the lookup files that Tilia uses to standardize taxonomy and other associated sample information.
+
+Navigating Tilia
+------------------------------------------------------------------------------
+
+While using Tilia there are some features that are found across the data input & manipulation process.  These include editing tools, the menu bar & menu icons, and formatting tools.
+
+Menu Bar
+````````````````````````````````````````````````````
+
+The menu bar is fixed.  It doesn't change, although options within individual (meta)data tabs can make options within individual menus selectable or not.
+
+File
+  Standard options:  Open, New, Close, Neotoma, Save, Save As, Export
+Edit
+  Standard options:  Undo, Cut, Copy, Copy All, Paste, Clear All, Format Cells, Formula to Value, Sort, Toggle Rare