[BP] Fixed typos, formatting and numbering (#7430)

* Fixed typos, formatting and numbering

* Fixed broken links in the Examples

* Renamed Readme.md to README.md

domain/README.md

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+# Domain Module
+
+The domain module contains the domain model object and the Spring-Data-JPA Repositories for accessing the database.  In order to
+compile correctly, you have to enable the JPA Metamodel generator.  It is an annotation processor and the instructions for enabling
+it in your IDE are available at: http://docs.jboss.org/hibernate/jpamodelgen/1.0/reference/en-US/html_single/#whatisit
+
+Maven already has it enabled, so if you don't want to work on this package, you only need to run the maven build and the
+required files will be generated.
+
+## Structure and Conventions
+
+The package structure of this module is to put:
+
+* JPA Entity and related Embeddable classes in the org.fao.geonet.domain package or sub-packages
+* JPA EntityListener objects in org.fao.geonet.entitylistener package or sub-packages
+* Spring-data repository objects in org.fao.geonet.repository package or sub-packages
+* Spring-data-jpa Specification Utility/Factory objects in org.fao.geonet.repository.specification package or sub-packages
+
+The file config-spring-geonetwork.xml in the src/main/resources directory configures spring and JPA to scan the
+org.fao.geonet.domain package (and sub-packages) for Entities and the org.fao.geonet.repository package for spring-data-jpa
+Repository objects.
+
+The exact list that is scanned by the spring configuration files needs to be checked.  At the time of this writing the file
+is config-spring-geonetwork.xml in this module.
+
+The side effect of this means that repositories and entities can be in other modules as well.  At the time of this writing
+that is not the case but should be considered in the future.
+
+## Writing Custom Queries
+
+IMPORTANT:  Please do not add any Specifications or Queries to the system without at least one test for each query!
+
+Spring Data allows four different ways to write queries. (For more in-depth explanation see: http://projects.spring.io/spring-data-jpa/
+
+1. Query methods
+   - You can create methods in the ...Repository interface and the method name will be parsed by Spring Data and a query will be created for you based on the name.  There are many different options including in, and, or ways to write the methods.
+   - While the methods are easy to write, they are not very flexible.  Using Specifications tends to be a more flexible solution and is therefore preferred.
+   - **Examples: (See tests for example usage)**
+     * [UserRepository](src/main/java/org/fao/geonet/repository/UserRepository.java)
+     * [OperationAllowedRepository](src/main/java/org/fao/geonet/repository/OperationAllowedRepository.java)
+2. Specifications
+   - The Specification interface provides a composable API for writing queries.
+   - For example, you could write a hasMetadataId specification and a hasOwnerId specification.  One could then compose them using not, and, or.
+   - Each specification should be in the appropriate <DomainObject>Specs class.
+   - Each specification is to be created with a static method.
+   - Each specification must have a test.
+   - **Examples: (See tests for example usage)**
+     * [MetadataSpecs](src/main/java/org/fao/geonet/repository/specification/MetadataSpecs.java)
+     * [UserSpecs](src/main/java/org/fao/geonet/repository/specification/UserSpecs.java)
+3. Custom Queries
+   - Spring JPA Repositories can have custom queries with very custom implementations.  A Repository will extend an interface with the custom methods and the implementations would be in a subclass of the interface.
+   - The implementation will use the normal EntityManager (JPA) API for constructing the queries.
+   - **Examples: (See tests for example usage)**
+     * [MetadataRepositoryCustom](src/main/java/org/fao/geonet/repository/MetadataRepositoryCustom.java)
+     * [MetadataRepositoryCustomImpl](src/main/java/org/fao/geonet/repository/MetadataRepositoryCustomImpl.java)
+4. Standard JPA querying
+   - One can obtain an EntityManager by using the @PersistentContext annotation on a field in a Spring bean.
+   - The EntityManager can be used to write queries.
+   - All Queries should be contained in the same module as the domain object that it is querying, unless the module is a plugin module.
+   - **Examples: (See tests for example usage)**
+     * [MetadataReportsQueries](src/main/java/org/fao/geonet/repository/reports/MetadataReportsQueries.java)