Remove duplicate documentation

Some parts of the usage section in the procedural knowledge learning chapter of the Soar manual were not included in the cli reference, thus they were moved.

Discussion see #41

Author: moschmdt

docs/reference/cli/cmd_chunk.md

@@ -118,6 +118,18 @@ This feature is not yet implemented.
 
 ## Preventing Possible Correctness Issues
 
+It is theoretically possible to detect nearly all of the sources of correctness
+issues and prevent rules from forming when those situations are detected. In
+Soar 9.6.0, though, only one filter is available, `allow-local-negations`. Future
+versions of Soar will include more correctness filters.
+
+Note that it is still possible to detect that your agent may have encountered a
+known source of a correctness issue by looking at the output of the chunk
+stats command. It has specific statistics for some of the sources, while others
+can be gleaned indirectly. For example, if the stats show that some rules
+required repair, you know that your agent testing or augmenting a previous
+result in a substate.
+
 ### chunk allow-local-negations
 
 The option `allow-local-negations` control whether or not chunks can be created

docs/reference/cli/cmd_explain.md

@@ -329,6 +329,49 @@ explainer will write out a file with the statistics when either Soar exits or a
 `soar init` is executed. This option is still considered experimental and in
 beta.
 
+## Explaining Learned Procedural Knowledge
+
+While explanation-based chunking makes it easier for people to now incorporate
+learning into their agents, the complexity of the analysis it performs makes it
+far more difficult to understand how the learned rules were formed. The
+explainer is a new module that has been developed to help ameliorate this
+problem. The explainer allows you to interactively explore how rules were
+learned.
+
+When requested, the explainer will make a very detailed record of everything
+that happened during a learning episode. Once a user specifies a recorded chunk
+to "discuss", they can browse all of the rule firings that contributed to the
+learned rule, one at a time. The explainer will present each of these rules with
+detailed information about the identity of the variables, whether it tested
+knowledge relevant to the the superstate, and how it is connected to other rule
+firings in the substate. Rule firings are assigned IDs so that user can quickly
+choose a new rule to examine.
+
+The explainer can also present several different screens that show more verbose
+analyses of how the chunk was created. Specifically, the user can ask for a
+description of (1) the chunk’s initial formation, (2) the identities of
+variables and how they map to identity sets, (3) the constraints that the
+problem-solving placed on values that a particular identity can have, and (4)
+specific statistics about that chunk, such as whether correctness issues were
+detected or whether it required repair to make it fully operational.
+
+Finally, the explainer will also create the data necessary to visualize all of
+the processing described in an image using the new ’visualize’ command. These
+visualization are the easiest way to quickly understand how a rule was formed.
+
+Note that, despite recording so much information, a lot of effort has been put
+into minimizing the cost of the explainer. When debugging, we often let it
+record all chunks and justifications formed because it is efficient enough to do
+so.
+
+Use the explain command without any arguments to display a summary of which rule
+firings the explainer is watching. It also shows which chunk or justification
+the user has specified is the current focus of its output, i.e. the chunk being
+discussed.
+
+Tip: This is a good way to get a chunk id so that you don’t have to type or
+paste in a chunk name.
+
 ## Visualizing an Explanation
 
 Soar's `visualize` command allows you to create images that represent processing

docs/reference/cli/cmd_visualize.md

@@ -104,7 +104,7 @@ applies to visualizing memory systems.
 ## File Handling Settings
 
 `file-name` specifies the base file name that Soar will use when creating both
-graphviz data files and images. You can specify a path as well, for example
+Graphviz data files and images. You can specify a path as well, for example
 "visualization/soar_viz", but make sure the directory exists first!
 
 `use-same-file` tells the visualizer to always overwrite the same files for each
@@ -114,7 +114,7 @@ command does not yet handle file creation as robustly as it could. If the file
 already exists, it will simply overwrite it rather than looking for a new file
 name.
 
-`generate-image` specifies whether the visualizer should render the graphviz
+`generate-image` specifies whether the visualizer should render the Graphviz
 file into an image. This setting is overridden if the viewer-launch setting is
 enabled.
 
@@ -144,6 +144,12 @@ Note that your operating system chooses which program to launch based on the
 file type. This feature has not been tested extensively on other platforms.
 Certain systems may not allow Soar to launch an external program.
 
+???+ note
+    For the visualizer to work, you must have Graphviz and DOT installed, which are
+    free third-party tools, and both must be available on your path. To date, the
+    visualizer has only been tested on Mac and Linux. It is possible that certain
+    systems may not allow Soar to launch an external program.
+
 ## See Also
 
 -   [explain](./cmd_explain.md)