Move running nexus docs up and fix docker compose file (#5230)

* Move running nexus docs up and fix docker compose file

---------

Co-authored-by: Simon Dumas <simon.dumas@epfl.ch>

docs/src/main/paradox/docs/delta/api/files-api.md

@@ -467,7 +467,7 @@ Request (metadata)
 Response  (metadata)
 :   @@snip [fetched-metadata.json](assets/files/fetched-metadata.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch tags

docs/src/main/paradox/docs/delta/api/projects-api.md

@@ -253,7 +253,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/projects/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the project will be returned.
 
 ## Fetch (specific version)

docs/src/main/paradox/docs/delta/api/resolvers-api.md

@@ -210,7 +210,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/resolvers/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/resources-api.md

@@ -327,7 +327,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/resources/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/schemas-api.md

@@ -247,7 +247,7 @@ Request
 Response
 :   @@snip [schema-fetched.json](assets/schemas/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/search-api.md

@@ -15,7 +15,7 @@ The search plugin relies on @ref:[composite views](./views/composite-view-api.md
   indices to which user has access to, i.e. has `views/query` permission.
 
 For instructions on how to configure global search in Nexus and how it works please visit the
-@ref:[Search configuration](../../getting-started/running-nexus/search-configuration.md) page.
+@ref:[Search configuration](../../running-nexus/search-configuration.md) page.
 
 @@@ note { .tip title="Api Mapping" }
 

docs/src/main/paradox/docs/delta/api/storages-api.md

@@ -221,7 +221,7 @@ Request
 Response
 :   @@snip [fetched.json](assets/storages/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/supervision-api.md

@@ -64,7 +64,7 @@ and the number of triples per individual view.
 The unassigned part allows to spot orphan namespaces, that is to say namespaces which may not have been properly deleted
 when a view got modified or deprecated.
 
-This is an indicator which helps to scale correctly the @ref:[Blazegraph instance](../../getting-started/running-nexus/blazegraph.md).
+This is an indicator which helps to scale correctly the @ref:[Blazegraph instance](../../running-nexus/blazegraph.md).
 
 ```
 GET /v1/supervision/blazegraph

docs/src/main/paradox/docs/delta/api/views/composite-sink.md

@@ -16,7 +16,7 @@ selected via configuration.
 
 By default, Nexus Delta will use the Single Composite Sink. This sink performs one query to the Blazegraph common namespace for each resource in the project. The queries are done in chronological order (by the `updatedAt` time of the resources).
 
-We recommend reading through the @ref:[search configuration example use case](../../../getting-started/running-nexus/search-configuration.md#example-use-case) and the @ref[Composite View API reference](composite-view-api.md) to learn more about Composite Views.
+We recommend reading through the @ref:[search configuration example use case](../../../running-nexus/search-configuration.md#example-use-case) and the @ref[Composite View API reference](composite-view-api.md) to learn more about Composite Views.
 
 ## Batch Composite Sink
 

docs/src/main/paradox/docs/delta/api/views/composite-view-api.md

@@ -500,7 +500,7 @@ Request
 Response
 :   @@snip [fetched.json](../assets/views/composite/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/delta/api/views/elasticsearch-view-api.md

@@ -332,7 +332,7 @@ Request
 Response
 :   @@snip [fetched.json](../assets/views/elasticsearch/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 Note that for retro-compatibility purposes, fetching an elasticsearch view returns legacy fields.

docs/src/main/paradox/docs/delta/api/views/sparql-view-api.md

@@ -211,7 +211,7 @@ Request
 Response
 :   @@snip [fetched.json](../assets/views/blazegraph/sparql/fetched.json)
 
-If the @ref:[redirect to Fusion feature](../../../getting-started/running-nexus/configuration/index.md#fusion-configuration) is enabled and
+If the @ref:[redirect to Fusion feature](../../../running-nexus/configuration/index.md#fusion-configuration) is enabled and
 if the `Accept` header is set to `text/html`, a redirection to the fusion representation of the resource will be returned.
 
 ## Fetch original payload

docs/src/main/paradox/docs/faq.md

@@ -17,8 +17,8 @@ There are many ways to run Nexus. Our public Sandbox is running @link:[here](htt
 and you can use it to test Nexus on small, non-sensitive data. Our @ref:[tutorial](getting-started/try-nexus.md) can 
 help you to run Nexus step by step.
 
-Meanwhile if you want to run it locally you can do so using @ref:[Docker](getting-started/running-nexus/index.md#docker). You can also deploy Nexus 
-@ref:[“on premise”](getting-started/running-nexus/index.md#on-premise-cloud-deployment), as a single instance or as a cluster. 
+Meanwhile if you want to run it locally you can do so using @ref:[Docker](running-nexus/index.md#docker). You can also deploy Nexus 
+@ref:[“on premise”](running-nexus/index.md#on-premise-cloud-deployment), as a single instance or as a cluster. 
 Blue Brain Nexus has also been deployed and tested on AWS using @link:[Kubernetes](https://kubernetes.io/){ open=new }.
 
 ### How can I try Blue Brain Nexus without installing it? 
@@ -75,7 +75,7 @@ There are several channels provided to address different issues:
 
 On macOS and Windows, Docker effectively runs containers inside a VM created by the system hypervisor. Nexus requires 
 at least 2 CPUs and 8 GB of memory in total. You can increase the limits in Docker settings in the menu 
-_Preferences > Advanced_. More details are in the dedicated @ref:[page](getting-started/running-nexus/index.md).
+_Preferences > Advanced_. More details are in the dedicated @ref:[page](running-nexus/index.md).
 
 ### What is JSON-LD?
 

docs/src/main/paradox/docs/getting-started/index.md

@@ -3,7 +3,6 @@
 - @ref:[Understanding Knowledge Graphs](understanding-knowledge-graphs.md)
 - @ref:[Neuroscience Tutorial](try-nexus.md)
 - @ref:[MovieLens Tutorial](try-nexus-movielens.md)
-- @ref:[Running Nexus](running-nexus/index.md)
 
 @@@
 
@@ -13,4 +12,4 @@ The Nexus ecosystem is a data catalog with several technologies and techniques u
 
 One of the powerful ways to query data is through the Knowledge Graph built in Nexus. For that reason we encourage you to get familiar with these concepts reading @ref:[Understanding Knowledge Graphs](understanding-knowledge-graphs.md).
 
-The next steps would be to either try Nexus using the @ref:[Sandbox](try-nexus.md) deployment or @ref:[run Nexus locally](running-nexus/index.md).
+The next steps would be to either try Nexus using the @ref:[Sandbox](try-nexus.md) deployment or @ref:[run Nexus locally](../running-nexus/index.md).

docs/src/main/paradox/docs/getting-started/try-nexus.md

@@ -116,7 +116,7 @@ You will need the names of the organisation and project for the next parts of th
 
 ### 1.2. Running your Own Instance of Nexus
 
-We do not recommend to setup your own instance for this tutorial. If you are interested to install your own instance, @ref:[check our guide](./running-nexus/index.md).
+We do not recommend to setup your own instance for this tutorial. If you are interested to install your own instance, @ref:[check our guide](../running-nexus/index.md).
 
 ## Step 2: Download and Register Data from a Single Source
 

docs/src/main/paradox/docs/index.md

@@ -2,6 +2,7 @@
 
 - [Versions](versions.md)
 - [Quick Start Guide](getting-started/index.md)
+- [Running Nexus](running-nexus/index.md)
 - [Releases](releases/index.md)
 - [Roadmap](roadmap.md)
 - [Nexus Fusion](fusion/index.md)
@@ -67,7 +68,7 @@ Do you know know what a knowledge graph is? Or want to deepen your understanding
 Want to get started with Nexus right away? We provide a @ref:[tutorial](getting-started/try-nexus.md) that uses our 
 @link:[sandbox](https://sandbox.bluebrainnexus.io/){ open=new } environment to let you try the functionalities.
 
-Ready to deploy your own instance of Nexus? Follow our @ref:[guide](getting-started/running-nexus/index.md).
+Ready to deploy your own instance of Nexus? Follow our @ref:[guide](running-nexus/index.md).
 
 ## Versions
 

docs/src/main/paradox/docs/releases/v1.11-release-notes.md

@@ -26,7 +26,7 @@ Nexus now supports conditional requests.
 
 Nexus now allows to provision realms at start up so as to simplify automated deployments.
 
-@ref[More here](../getting-started/running-nexus/configuration/index.md#realm-provisioning)
+@ref[More here](../running-nexus/configuration/index.md#realm-provisioning)
 
 ### Remote storage server
 

docs/src/main/paradox/docs/releases/v1.6-release-notes.md

@@ -12,7 +12,7 @@ visit the @ref:[migration instructions](v1.5-to-v1.6-migration.md) for the neces
 
 ## Nexus Delta
 
-The main goal of this release is to allow users to search across multiple projects through @ref:[global search](../getting-started/running-nexus/search-configuration.md)
+The main goal of this release is to allow users to search across multiple projects through @ref:[global search](../running-nexus/search-configuration.md)
 
 Secondary goals include:
 
@@ -47,14 +47,14 @@ Global search is composed of 2 parts:
 - A Delta plugin which allows to index and query resources according to a given configuration
 - A matching plugin in Fusion allows to query the endpoints provided by Delta to filter/sort results and customize how these results are displayed to the users
 
-More details about search and how to configure it is provided @ref:[here](../getting-started/running-nexus/search-configuration.md)
+More details about search and how to configure it is provided @ref:[here](../running-nexus/search-configuration.md)
 
 Please note that this first version is experimental in both Delta and Fusion and that improvements and possibly breaking
 changes may be introduced in the upcoming releases.
 
 ### Secure the Delta Elasticsearch client
 
-With 1.6, it is now possible to define credentials to query a secured Elasticsearch cluster: @ref:[Elasticsearch configuration](../getting-started/running-nexus/configuration/index.md#elasticsearch-views-plugin-configuration).
+With 1.6, it is now possible to define credentials to query a secured Elasticsearch cluster: @ref:[Elasticsearch configuration](../running-nexus/configuration/index.md#elasticsearch-views-plugin-configuration).
 
 ### Dedicated Blazegraph client for user-defined queries
 
@@ -82,7 +82,7 @@ The RDF parser allowing to validate incoming data can now be @link:[configured](
 
 When enabled, a dedicated project is created for the current user on its first access to the Nexus platform.
 
-How to enable and configure it is detailed @ref:[here](../getting-started/running-nexus/configuration/index.md#automatic-project-provisioning)
+How to enable and configure it is detailed @ref:[here](../running-nexus/configuration/index.md#automatic-project-provisioning)
 
 ### Deletion of projects
 

docs/src/main/paradox/docs/releases/v1.7-release-notes.md

@@ -90,7 +90,7 @@ This change implies a @ref:[migration when updating Nexus Delta to 1.7](v1.6-to-
 
 Besides JVM properties and environment variables, Delta configuration can now be defined via a external file.
 
-@ref:[Read More about Delta configuration](../getting-started/running-nexus/configuration/index.md)
+@ref:[Read More about Delta configuration](../running-nexus/configuration/index.md)
 
 ### Deleting tags on resources
 

docs/src/main/paradox/docs/releases/v1.7-to-v1.8-migration.md

@@ -248,7 +248,7 @@ The following environment variables need to be set when launching Delta v1.8 in
 | S3 storage enabling         | plugins.storage.storages.amazon.enabled              | true/false            |
 
 For more information on the configuration of Delta, please refer to the
-@ref:[Nexus configuration page](../getting-started/running-nexus/configuration/index.md).
+@ref:[Nexus configuration page](../running-nexus/configuration/index.md).
 
 ## Migrating events from Cassandra to PostgreSQL
 

docs/src/main/paradox/docs/releases/v1.8-to-v1.9-migration.md

@@ -61,5 +61,5 @@ Currently, both remote storages and composite views with remote sources can hold
 
 A remote storage might currently have a token stored in the storage definition. In 1.9, this should be moved to `plugins.storage.storages.remote-disk.credentials`.
 
-A composite view might currently have a token stored in the view definition. In 1.9, this should be moved to `plugins.composite-views.remote-source-credentials`, as shown @ref:[here](../getting-started/running-nexus/configuration/index.md#composite-views-plugin-configuration)
+A composite view might currently have a token stored in the view definition. In 1.9, this should be moved to `plugins.composite-views.remote-source-credentials`, as shown @ref:[here](../running-nexus/configuration/index.md#composite-views-plugin-configuration)
 

docs/src/main/paradox/docs/releases/v1.9-release-notes.md

@@ -151,7 +151,7 @@ Preserving the intermediate space also reduces the fragmentation of the Blazegra
 
 Rather than storing an auth token in the composite view, it is now expected to specify an authentication method in the Delta configuration.
 
-@ref:[More information](../getting-started/running-nexus/configuration/index.md#composite-views-plugin-configuration)
+@ref:[More information](../running-nexus/configuration/index.md#composite-views-plugin-configuration)
 
 #### Remove the resourceTag field in projections of composite views
 
@@ -224,7 +224,7 @@ The automatic detection of the media type can now be customized at the Delta lev
 
 NB: The media type provided by the user still prevails over automatic detection.
 
-@ref:[More information](../getting-started/running-nexus/configuration/index.md#file-configuration)
+@ref:[More information](../running-nexus/configuration/index.md#file-configuration)
 
 #### Tagging at creation/update
 
@@ -307,7 +307,7 @@ The 1.9 release of Nexus Fusion focuses on enhancing user interaction, resource
 
 The Nexus storage app also benefits from the changes in automatic file detection.
 
-@ref:[More information](../getting-started/running-nexus/configuration/index.md#file-configuration)
+@ref:[More information](../running-nexus/configuration/index.md#file-configuration)
 
 ### Removing Delta callback to validate the caller identity
 

docs/src/main/paradox/docs/getting-started/running-nexus/blazegraph.md → docs/src/main/paradox/docs/running-nexus/blazegraph.md

@@ -38,8 +38,8 @@ It is likely to happen when reindexing after updating search but if it happens r
 Blazegraph will use the available RAM in 2 ways, JVM heap and the file system cache
 so like Elasticsearch, the JVM garbage collection frequency and duration are also important to monitor.
 
-Using the supervision endpoints for @ref:[Blazegraph](../../delta/api/supervision-api.md#blazegraph) 
-and @ref:[composite views](../../delta/api/supervision-api.md#composite-views) and 
+Using the supervision endpoints for @ref:[Blazegraph](../delta/api/supervision-api.md#blazegraph) 
+and @ref:[composite views](../delta/api/supervision-api.md#composite-views) and 
 the @link:[RAM guidance from Blazegraph](https://github.com/blazegraph/database/wiki/Hardware_Configuration#ram-sizing-guidance)
 gives some insights on how much memory can be assigned.
 
@@ -56,8 +56,8 @@ to reduce the disk usage, but it takes quite a bit a time and requires taking th
 An alternative can be to reindex on a fresh instance of Blazegraph, this approach also allows to reconfigure the
 underlying namespaces.
 
-Using the supervision endpoints for @ref:[Blazegraph](../../delta/api/supervision-api.md#blazegraph)
-and @ref:[composite views](../../delta/api/supervision-api.md#composite-views) and
+Using the supervision endpoints for @ref:[Blazegraph](../delta/api/supervision-api.md#blazegraph)
+and @ref:[composite views](../delta/api/supervision-api.md#composite-views) and
 the @link:[Data on disk guidance from Blazegraph](https://github.com/blazegraph/database/wiki/Hardware_Configuration#data-on-disk-sizing-guidance)
 gives some insights on how much storage can be assigned.
 

docs/src/main/paradox/docs/getting-started/running-nexus/configuration/index.md → docs/src/main/paradox/docs/running-nexus/configuration/index.md

@@ -59,7 +59,7 @@ Nexus Delta uses a service account to perform automatic tasks under the hood. Ex
 
 Realm provisioning allows to create one or several realm at startup.
 
-It is useful to start a new deployment with having to call the @ref:[realm API](../../../delta/api/realms-api.md) to create those.
+It is useful to start a new deployment with having to call the @ref:[realm API](../../delta/api/realms-api.md) to create those.
 
 Exemple:
 ```hocon
@@ -114,7 +114,7 @@ When fetching a resource, Nexus Delta allows to return a redirection to its repr
 
 ## Projections configuration
 
-Projections in Nexus Delta are asynchronous processes that can replay the event log and process this information. For more information on projections, please refer to the @ref:[Architecture page](../../../delta/architecture.md).
+Projections in Nexus Delta are asynchronous processes that can replay the event log and process this information. For more information on projections, please refer to the @ref:[Architecture page](../../delta/architecture.md).
 
 @link:[The `projections` section](https://github.com/BlueBrain/nexus/blob/$git.branch$/delta/app/src/main/resources/app.conf#L281) of the configuration allows to configure the projections.
 
@@ -126,7 +126,7 @@ Since 1.5.0, Nexus Delta supports plugins. Jar files present inside the local di
 
 Each plugin configuration is rooted under `plugins.{plugin_name}`. All plugins have a `plugins.{plugin_name}.priority` configuration flag used to determine the order in which the routes are handled in case of collisions. 
 
-For more information about plugins, please refer to the @ref:[Plugins page](../../../delta/plugins/index.md).
+For more information about plugins, please refer to the @ref:[Plugins page](../../delta/plugins/index.md).
 
 ### Elasticsearch views plugin configuration