Clearing up status of notebooks and R Markdown files

DESIGN.md

@@ -64,12 +64,13 @@ this template is organized the way it is:
     order for the lesson to be displayed properly on GitHub.
 
     It's also considered bad practice to put generated files in the
-    same directory as source files.  We do it because some source
-    files, such as R Markdown and IPython Notebook files, are
-    executable, and contain paths to things like images and data
-    files.  If we put our source files in a sub-directory, those paths
-    won't work (or conversely, if we put our generated files in a
-    different directory, the paths won't work there).
+    same directory as source files.  We do it because some authors may
+    use auxiliary source files such as R Markdown and IPython Notebook
+    files which are executable, and contain paths to things like
+    images and data files.  If we put our source files in a
+    sub-directory, those paths won't work (or conversely, if we put
+    our generated files in a different directory, the paths won't work
+    there).
 
 7.  In order to display properly, our generated HTML pages need
     artwork, CSS style files, and a few bits of Javascript.  We could

LAYOUT.md

@@ -7,9 +7,9 @@ submodules or clever tricks with symbolic links).
 1.  `README.md`: initially a copy of this file.  It should be
     overwritten with short description of the lesson.
 
-2.  Other files in the root directory: the source of the lesson's
-    web pages (and possibly also things like IPython Notebooks and
-    R Markdown files that those pages are generated from).
+2.  Other files in the root directory: the source of the lesson's web
+    pages (and possibly auxiliary files like IPython Notebooks and R
+    Markdown files).
 
 3.  `code/`, `data/`, and `fig/`: sub-directories containing sample
     code, data files, and figures.  See "Code, Data, and Figures"
@@ -43,7 +43,9 @@ plots, and diagrams used in the lessons must go in a `fig/` directory.
     directory, not the `data` directory).
 
 2.  IPython Notebooks and R Markdown files, which are both code and
-    the source for web pages, should go in the root directory.
+    the source for web pages, should go in the root directory.  These
+    will not be checked by our validation tool, or indexed by other
+    tools we plan to build.
 
 3.  We strongly prefer SVG for line drawings, since they are smaller,
     scale better, and are easier to edit. Screenshots and other raster