first cut at docs re-org (#680)

* first cut at docs re-org

* second pass at docs reorg

* update cross-references

Author: rosemarymarano

README.md

@@ -21,15 +21,15 @@ To have the Create Domain Tool run RCU, simply add the `-run_rcu` argument to th
 
 It is also possible to specify the connection information in the model instead of using the command-line arguments.  This is especially easier for databases that require complex database connection string and extra parameters, such as RAC or Oracle Autonomous Transaction Processing Cloud Service database.  For information on how to use it, refer to [Specifying RCU connection information in the model](rcuinfo.md)
 
-To create more complex domains, it may be necessary to create a custom domain type. This is useful for cases where the domain has custom templates, or templates for other Oracle products. For more information, refer to [Domain Type Definitions](type_def.md).
+To create more complex domains, it may be necessary to create a custom domain type. This is useful for cases where the domain has custom templates, or templates for other Oracle products. For more information, refer to [Domain Type Definitions](tool_configuration.md#domain-type-definitions).
 
 ### Using an Encrypted Model
 
 If the model or variables file contains passwords encrypted with the WDT Encryption tool, decrypt the passwords during create with the `-use_encryption` flag on the command line to tell the Create Domain Tool that encryption is being used and to prompt for the encryption passphrase.  As with the database passwords, the tool can also read the passphrase from standard input (for example, `stdin`) to allow the tool to run without any user input.
 
 ### Using Multiple Models
 
-The Create Domain Tool supports the use of multiple models, as described in [Using Multiple Models](../README.md#using-multiple-models).
+The Create Domain Tool supports the use of multiple models, as described in [Using Multiple Models](model.md#using-multiple-models).
 
 ### Development Domain and `boot.properties`
 

site/create.md

@@ -35,4 +35,4 @@ If the model or variables file contains passwords encrypted with the WDT Encrypt
 
 ### Using Multiple Models
 
-The Deploy Applications Tool supports the use of multiple models, as described in [Using Multiple Models](../README.md#using-multiple-models).
+The Deploy Applications Tool supports the use of multiple models, as described in [Using Multiple Models](model.md#using-multiple-models).

site/deploy.md

@@ -13,36 +13,38 @@ When creating the archive, the tool will try to gather all binaries, scripts, an
 1. Any binaries referenced from the `ORACLE_HOME` will not be gathered, as they are assumed to exist in any target domain to which model-driven operations will be applied.  Doing this is key to allowing the model to be WebLogic Server version independent.
 2. In its current form, the Discover Domain Tool will only gather binaries and scripts that are accessible from the local machine.  Warnings will be generated for any binaries or scripts that cannot be found but the configuration for those binaries will still be collected, where possible.  It is the user's responsibility to add those missing files to the archive in the appropriate locations and edit the the model, as needed, to point to those files inside the archive using the relative path inside the archive (for example, `wlsdeploy/applications/myapp.ear`).
 
-You can customize what is generated in the model for password attributes by providing a variable file location and name. This file is a text properties file which will contain a key=value for each password found in the model. The key is a unique token name for a password attribute, and the value is the replacement value; in this case, an empty string. The attribute in the model is injected with the token name and property field notation. For example, `@@PROP:AdminUserName@@` or `@@PROP:JDBCSystemResource.<Name>.JdbcResource.JDBCDriverParams.PasswordEncrypted@@`. 
+You can customize what is generated in the model for password attributes by providing a variable file location and name. This file is a text properties file which will contain a key=value for each password found in the model. The key is a unique token name for a password attribute, and the value is the replacement value; in this case, an empty string. The attribute in the model is injected with the token name and property field notation. For example, `@@PROP:AdminUserName@@` or `@@PROP:JDBCSystemResource.<Name>.JdbcResource.JDBCDriverParams.PasswordEncrypted@@`.
 
 A command line example containing the variable file name:
 
     weblogic-deploy\bin\discoverDomain.cmd -oracle_home c:\wls12213 -domain_home domains\DemoDomain -archive_file DiscoveredDemoDomain.zip -model_file DiscoveredDemoDomain.json -variable_file DiscoverDemoDomain.properties
-    
-To discover the domain using online WLST, simply include the admin user name and admin URL on the command line. The tool will prompt for a password to be entered into STDIN. 
+
+To discover the domain using online WLST, simply include the admin user name and admin URL on the command line. The tool will prompt for a password to be entered into STDIN.
 
 An example of running in online WLST mode:
 
     weblogic-deploy/bin/discoverDomain.sh -oracle_home /u01/oracle -domain_home /u01/oracle/domains/DemoDomain -archive_file ./DiscoveredDemoDomain.zip -model_file ./DiscoveredDemoDomain.yaml -admin_user weblogic -admin_url t3://localhost:7001
 
 Note that the command must run on the same system where the domain binaries are located in order to successfully gather the corresponding binaries into the archive file.
 
-When a domain is created using custom or product templates, the templates will install resources into the domain that do not need to be discovered for the model or collected into the archive. The domain type argument, which corresponds to a domain typedef file, must describe the type of domain in order for these resources and files to be ignored. By default, discover runs using domain type WLS, which assumes only the WebLogic Server template was applied to the domain. The tool has canned typedefs for two other domain types, RestrictedJRF and JRF. You may use these domain types, or another custom typedef. For more information, refer to [Domain Type Definitions](type_def.md).
+When a domain is created using custom or product templates, the templates will install resources into the domain that do not need to be discovered for the model or collected into the archive. The domain type argument, which corresponds to a domain typedef file, must describe the type of domain in order for these resources and files to be ignored. By default, discover runs using domain type WLS, which assumes only the WebLogic Server template was applied to the domain. The tool has canned typedefs for two other domain types, RestrictedJRF and JRF. You may use these domain types, or another custom typedef. For more information, refer to [Domain Type Definitions](tool_configuration.md#domain-type-definitions).
 
 An example of using the domain type argument:
-    
+
     weblogic-deploy\bin\discoverDomain.cmd -oracle_home c:\wls12213 -domain_home domains\DemoDomain -archive_file DiscoveredDemoDomain.zip -model_file DiscoveredDemoDomain.yaml -domain_type RestrictedJRF
-    
+
 Before the model is persisted to the model file, any variable injectors or model filters are run, in that order. The final step is validation, which validates the contents of the model, archive and variable file. If the validation is successful, the model is persisted. For more information on these three topics, go to:
 
  - [Variable Injection](variable_injection.md)
- - [Model Filters](tool_filters.md)
+ - [Model Filters](tool_configuration.md#model-filters)
  - [Validate Model Tool](validate.md)
 
+
 The resulting model can also be modified for compatibility with specific target environments, such as Oracle Weblogic Server Kubernetes Operator. For more information, see [Target Environments](config/target_env.md).
 
 Any problems (or success) will be listed in the discover tool summary. The summary will print the version of the tool and Oracle home, and the WLST mode with which the tool was run (online or offline). A recap of all Warning and Severe messages will be listed, along with a total. 
 
+
 An example of a summary with a WARNING message:
 
 ```
@@ -59,7 +61,7 @@ Total:       WARNING :     1    SEVERE :     0
 The following environment variables may be set.
 
 -  JAVA_HOME             The location of the JDK. This must be a valid Java 7 or later JDK.
--  WLSDEPLOY_HOME        The location of the WebLogic Deploy Tooling installation. By default, the location is calculated 
+-  WLSDEPLOY_HOME        The location of the WebLogic Deploy Tooling installation. By default, the location is calculated
                          from the location of the discoverDomain script.
 -  WLSDEPLOY_PROPERTIES  System properties that will be passed to WLST.
 

site/discover.md

@@ -55,7 +55,7 @@ kubernetes:
                 JAVA_OPTIONS:
                     value: '-Dmydir=/home/me'
 ```
-This example uses `@@PROP:mySecret@@` to pull the value for `webLogicCredentialsSecret` from the variables file specified on the command line. This can be done with any of the values in the `kubernetes` section of the model. More details about using model variables can be found [here](../README.md/#simple-example).
+This example uses `@@PROP:mySecret@@` to pull the value for `webLogicCredentialsSecret` from the variables file specified on the command line. This can be done with any of the values in the `kubernetes` section of the model. More details about using model variables can be found [here](model.md#simple-example).
 
 For this example, the resulting domain resource file would contain:
 ```yaml
@@ -88,11 +88,11 @@ The syntax of the `spec/serverPod/env` and other list sections in the WDT model
 
 If clusters are specified in the `kubernetes/spec` section of the model, those clusters will be configured in the domain resource file, and clusters from the `topology` section will be disregarded.
 
-If the WDT model has a value of `Never` for `spec/imagePullPolicy`, the `imagePullSecrets` default value will not be added. 
- 
+If the WDT model has a value of `Never` for `spec/imagePullPolicy`, the `imagePullSecrets` default value will not be added.
+
 A full list of sections and variables supported by the Oracle WebLogic Server Kubernetes Operator is available [here](https://github.com/oracle/weblogic-kubernetes-operator/blob/master/docs/domains/Domain.md).
 
-The Extract Domain Resource Tool supports a subset of these sections, including `metadata`, `serverPod`, and `spec`. 
+The Extract Domain Resource Tool supports a subset of these sections, including `metadata`, `serverPod`, and `spec`.
 
 The [Model Help Tool](model_help.md) can be used to determine the folders and attributes that can be used in the `kubernetes` section of the model. For example, this command will list the folders and attributes in the `spec` folder:
 ```yaml