Update file handling doc. Fixes projectatomic#285

docs/file_handling.md

@@ -1,18 +1,42 @@
 ## Fetch
 
-Fetching an Atomic App means to download the artifacts and sample answerfile.
+Fetching an Atomic App means to download the metadata files: artifacts and
+sample answerfile for an atomic app. By default, it downloads the metadata
+files for the atomicapp to a directory of the form
+``/var/lib/atomicapp/<atomicapp name>-<uuid>``. If needed,
+you can also specify a target directory to download the metadata for the
+atomic app using the ``--destination`` option.
 
 ## Developing and Debugging
 
 Image developers may run the root container and point to a Nulecule directory on the local system.
 
 ## Directories
 
-* `/tmp/<atomicapp_name>`: Host directory for temporary Nulecule files. May be overridden.
-* `/tmp/<atomicapp_name>/.workdir`: Host directory for artifact template files with variable substitution.
+* `external/`: External atomic apps, if any, for the given atomic app are
+    fetched into ``external`` directory inside the directory of
+    the atomic app, during, fetching the atomic app with
+    dependencies or running the atomic app.
+* `/var/lib/atomicapp/<atomic app name>-<uuid>`: This is where an atomic app
+    and it's dependencies are fetched when fetching or running the atomic app,
+    unless, a specific destination is specified.
 
 ## Artifact path
 
 Local path to an artifact file or a directory containing artifact files as its
 immediate children.
 
+## Runtime answers file
+
+When running an atomic app, it asks the users for missing values for
+parameters defined in the atomic app and it's child atomic apps. This
+aggregated answers data is used to run the atomic app, and is dumped
+to a file: ``answers.conf.gen`` in the atomic app's directory, to be
+used later when stopping the atomic app.
+
+## Rendered artifact files
+
+Artifact files are rendered with runtime answers data along side the original
+artifact files, but with the filenames prefixed with a `.` (dot), to make
+them hidden.
+