[QC-1286] Refactor doc

README.md

@@ -17,23 +17,18 @@ For a general overview of our (O2) software, organization and processes, please
         * [Environment loading](doc/QuickStart.md#environment-loading)
     * [Execution](doc/QuickStart.md#execution)
         * [Basic workflow](doc/QuickStart.md#basic-workflow)
-        * [Readout chain (optional)](doc/QuickStart.md#readout-chain-optional)
         * [Post-processing example](doc/QuickStart.md#post-processing-example)
 * [Modules development](doc/ModulesDevelopment.md)
     * [Context](doc/ModulesDevelopment.md#context)
         * [QC architecture](doc/ModulesDevelopment.md#qc-architecture)
         * [DPL](doc/ModulesDevelopment.md#dpl)
         * [Data Sampling](doc/ModulesDevelopment.md#data-sampling)
-            * [Custom Data Sampling Condition](doc/ModulesDevelopment.md#custom-data-sampling-condition)
-            * [Bypassing the Data Sampling](doc/ModulesDevelopment.md#bypassing-the-data-sampling)
         * [Code Organization](doc/ModulesDevelopment.md#code-organization)
         * [Developing with aliBuild/alienv](doc/ModulesDevelopment.md#developing-with-alibuildalienv)
         * [User-defined modules](doc/ModulesDevelopment.md#user-defined-modules)
         * [Repository](doc/ModulesDevelopment.md#repository)
-            * [Paths](doc/ModulesDevelopment.md#paths)
     * [Module creation](doc/ModulesDevelopment.md#module-creation)
     * [Test run](doc/ModulesDevelopment.md#test-run)
-        * [Saving the QC objects in a local file](doc/ModulesDevelopment.md#saving-the-qc-objects-in-a-local-file)
     * [Modification of the Task](doc/ModulesDevelopment.md#modification-of-the-task)
     * [Check](doc/ModulesDevelopment.md#check)
         * [Configuration](doc/ModulesDevelopment.md#configuration)
@@ -46,81 +41,73 @@ For a general overview of our (O2) software, organization and processes, please
     * [Naming convention](doc/ModulesDevelopment.md#naming-convention)
     * [Committing code](doc/ModulesDevelopment.md#committing-code)
     * [Data sources](doc/ModulesDevelopment.md#data-sources)
-        * [Readout](doc/ModulesDevelopment.md#readout)
-        * [DPL workflow](doc/ModulesDevelopment.md#dpl-workflow)
     * [Run number and other run attributes (period, pass type, provenance)](doc/ModulesDevelopment.md#run-number-and-other-run-attributes-period-pass-type-provenance)
     * [A more advanced example](doc/ModulesDevelopment.md#a-more-advanced-example)
-    * [Monitoring](doc/ModulesDevelopment.md#monitoring)
+* [Framework](doc/Framework.md)
+    * [Plugging the QC to an existing DPL workflow](doc/Framework.md#plugging-the-qc-to-an-existing-dpl-workflow)
+    * [Production of QC objects outside this framework](doc/Framework.md#production-of-qc-objects-outside-this-framework)
+    * [Multi-node setups](doc/Framework.md#multi-node-setups)
+    * [Batch processing](doc/Framework.md#batch-processing)
+    * [Moving window](doc/Framework.md#moving-window)
+    * [Monitor cycles](doc/Framework.md#monitor-cycles)
+    * [Custom merging](doc/Framework.md#custom-merging)
+    * [Critical, resilient and non-critical tasks](doc/Framework.md#critical-resilient-and-non-critical-tasks)
+    * [QC with DPL Analysis](doc/Framework.md#qc-with-dpl-analysis)
+    * [Propagating Check results to RCT in Bookkeeping](doc/Framework.md#propagating-check-results-to-rct-in-bookkeeping)
+    * [Solving performance issues](doc/Framework.md#solving-performance-issues)
+    * [Understanding and reducing memory footprint](doc/Framework.md#understanding-and-reducing-memory-footprint)
+    * [Monitoring](doc/Framework.md#monitoring)
 * [Post-processing](doc/PostProcessing.md)
-    * [The post-processing framework](doc/PostProcessing.md#the-post-processing-framework)
-        * [Post-processing interface](doc/PostProcessing.md#post-processing-interface)
-        * [Configuration](doc/PostProcessing.md#configuration)
-    * [Definition and access of user-specific configuration](doc/PostProcessing.md#definition-and-access-of-user-specific-configuration)
-        * [Running it](doc/PostProcessing.md#running-it)
-    * [Convenience classes](doc/PostProcessing.md#convenience-classes)
-        * [The TrendingTask class](doc/PostProcessing.md#the-trendingtask-class)
-        * [The SliceTrendingTask class](doc/PostProcessing.md#the-slicetrendingtask-class)
-        * [The QualityTask class](doc/PostProcessing.md#the-qualitytask-class)
-        * [The BigScreen class](doc/PostProcessing.md#the-bigscreen-class)
-    * [More examples](doc/PostProcessing.md#more-examples)
-* [Advanced topics](doc/Advanced.md)
-  * [Framework](doc/Advanced.md#framework)
-      * [Plugging the QC to an existing DPL workflow](doc/Advanced.md#plugging-the-qc-to-an-existing-dpl-workflow)
-      * [Production of QC objects outside this framework](doc/Advanced.md#production-of-qc-objects-outside-this-framework)
-      * [Multi-node setups](doc/Advanced.md#multi-node-setups)
-      * [Batch processing](doc/Advanced.md#batch-processing)
-      * [Moving window](doc/Advanced.md#moving-window)
-      * [Monitor cycles](doc/Advanced.md#monitor-cycles)
-      * [Writing a DPL data producer](doc/Advanced.md#writing-a-dpl-data-producer)
-      * [Custom merging](doc/Advanced.md#custom-merging)
-      * [Critical, resilient and non-critical tasks](doc/Advanced.md#critical-resilient-and-non-critical-tasks)
-      * [QC with DPL Analysis](doc/Advanced.md#qc-with-dpl-analysis)
-          * [Uploading objects to QCDB](doc/Advanced.md#uploading-objects-to-qcdb)
-      * [Propagating Check results to RCT in Bookkeeping](doc/Advanced.md#propagating-check-results-to-rct-in-bookkeeping)
-          * [Conversion details](doc/Advanced.md#conversion-details)
-  * [Solving performance issues](doc/Advanced.md#solving-performance-issues)
-      * [Dispatcher](doc/Advanced.md#dispatcher)
-      * [QC Tasks](doc/Advanced.md#qc-tasks-1)
-      * [Mergers](doc/Advanced.md#mergers)
-  * [Understanding and reducing memory footprint](doc/Advanced.md#understanding-and-reducing-memory-footprint)
-      * [Analysing memory usage with valgrind](doc/Advanced.md#analysing-memory-usage-with-valgrind)
-  * [CCDB / QCDB](doc/Advanced.md#ccdb--qcdb)
-      * [Accessing objects in CCDB](doc/Advanced.md#accessing-objects-in-ccdb)
-      * [Access GRP objects with GRP Geom Helper](doc/Advanced.md#access-grp-objects-with-grp-geom-helper)
-      * [Global Tracking Data Request helper](doc/Advanced.md#global-tracking-data-request-helper)
-      * [Custom metadata](doc/Advanced.md#custom-metadata)
-      * [Details on the data storage format in the CCDB](doc/Advanced.md#details-on-the-data-storage-format-in-the-ccdb)
-      * [Local CCDB setup](doc/Advanced.md#local-ccdb-setup)
-      * [Instructions to move an object in the QCDB](doc/Advanced.md#instructions-to-move-an-object-in-the-qcdb)
-  * [Asynchronous Data and Monte Carlo QC operations](doc/Advanced.md#asynchronous-data-and-monte-carlo-qc-operations)
-  * [QCG](doc/Advanced.md#qcg)
-      * [Display a non-standard ROOT object in QCG](doc/Advanced.md#display-a-non-standard-root-object-in-qcg)
-      * [Canvas options](doc/Advanced.md#canvas-options)
-      * [Local QCG (QC GUI) setup](doc/Advanced.md#local-qcg-qc-gui-setup)
-  * [FLP Suite](doc/Advanced.md#flp-suite)
-      * [Developing QC modules on a machine with FLP suite](doc/Advanced.md#developing-qc-modules-on-a-machine-with-flp-suite)
-      * [Switch detector in the workflow <em>readout-dataflow</em>](doc/Advanced.md#switch-detector-in-the-workflow-readout-dataflow)
-      * [Get all the task output to the infologger](doc/Advanced.md#get-all-the-task-output-to-the-infologger)
-      * [Using a different config file with the general QC](doc/Advanced.md#using-a-different-config-file-with-the-general-qc)
-      * [Enable the repo cleaner](doc/Advanced.md#enable-the-repo-cleaner)
-  * [Configuration](doc/Advanced.md#configuration-1)
-      * [Merging multiple configuration files into one](doc/Advanced.md#merging-multiple-configuration-files-into-one)
-      * [Definition and access of simple user-defined task configuration ("taskParameters")](doc/Advanced.md#definition-and-access-of-simple-user-defined-task-configuration-taskparameters)
-      * [Definition and access of user-defined configuration ("extendedTaskParameters")](doc/Advanced.md#definition-and-access-of-user-defined-configuration-extendedtaskparameters)
-      * [Definition of new arguments](doc/Advanced.md#definition-of-new-arguments)
-      * [Configuration files details](doc/Advanced.md#configuration-files-details)
-          * [Global configuration structure](doc/Advanced.md#global-configuration-structure)
-          * [Common configuration](doc/Advanced.md#common-configuration)
-          * [QC Tasks configuration](doc/Advanced.md#qc-tasks-configuration)
-          * [QC Checks configuration](doc/Advanced.md#qc-checks-configuration)
-          * [QC Aggregators configuration](doc/Advanced.md#qc-aggregators-configuration)
-          * [QC Post-processing configuration](doc/Advanced.md#qc-post-processing-configuration)
-          * [External tasks configuration](doc/Advanced.md#external-tasks-configuration)
-  * [Miscellaneous](doc/Advanced.md#miscellaneous)
-      * [Data Sampling monitoring](doc/Advanced.md#data-sampling-monitoring)
-      * [Monitoring metrics](doc/Advanced.md#monitoring-metrics)
-      * [Common check IncreasingEntries](doc/Advanced.md#common-check-increasingentries)
-      * [Update the shmem segment size of a detector](doc/Advanced.md#update-the-shmem-segment-size-of-a-detector)
+    * [The post-processing framework](doc/PostProcessing#the-post-processing-framework)
+        * [Post-processing interface](doc/PostProcessing#post-processing-interface)
+        * [Configuration](doc/PostProcessing#configuration)
+        * [Running it](doc/PostProcessing#running-it)
+    * [Convenience classes](doc/PostProcessing#convenience-classes)
+        * [The TrendingTask class](doc/PostProcessing#the-trendingtask-class)
+        * [The SliceTrendingTask class](doc/PostProcessing#the-slicetrendingtask-class)
+        * [The ReferenceComparatorTask class](doc/PostProcessing#the-referencecomparatortask-class)
+        * [The CcdbInspectorTask class](doc/PostProcessing#the-ccdbinspectortask-class)
+        * [The QualityTask class](doc/PostProcessing#the-qualitytask-class)
+        * [The BigScreen class](doc/PostProcessing#the-bigscreen-class)
+    * [More examples](#more-examples)
+* [Configuration reference](doc/Configuration.md)
+    * [Global configuration structure](doc/Configuration.md#global-configuration-structure)
+    * [Common configuration](doc/Configuration.md#common-configuration)
+    * [QC Tasks configuration](doc/Configuration.md#qc-tasks-configuration)
+    * [QC Checks configuration](doc/Configuration.md#qc-checks-configuration)
+    * [QC Aggregators configuration](doc/Configuration.md#qc-aggregators-configuration)
+    * [QC Post-processing configuration](doc/Configuration.md#qc-post-processing-configuration)
+    * [External tasks configuration](doc/Configuration.md#external-tasks-configuration)
+    * [Merging multiple configuration files into one](doc/Configuration.md#merging-multiple-configuration-files-into-one)
+    * [Templating config files](doc/Configuration.md#templating-config-files)
+    * [Definition and access of simple user-defined task configuration ("taskParameters")](doc/Configuration.md#definition-and-access-of-simple-user-defined-task-configuration-taskparameters)
+    * [Definition and access of user-defined configuration ("extendedTaskParameters")](doc/Configuration.md#definition-and-access-of-user-defined-configuration-extendedtaskparameters)
+* [QCDB and CCDB](doc/QCDB.md)
+    * [QCDB vs CCDB](doc/QCDB.md#qcdb-vs-ccdb)
+    * [Details on the data storage format in the QCDB](doc/QCDB.md#details-on-the-data-storage-format-in-the-qcdb)
+    * [Custom metadata for QC objects in the QCDB](doc/QCDB.md#custom-metadata-for-qc-objects-in-the-qcdb)
+    * [Instructions to move an object in the QCDB](doc/QCDB.md#instructions-to-move-an-object-in-the-qcdb)
+    * [Accessing objects in CCDB](doc/QCDB.md#accessing-objects-in-ccdb)
+    * [Access GRP objects with GRP Geom Helper](doc/QCDB.md#access-grp-objects-with-grp-geom-helper)
+    * [Global Tracking Data Request helper](doc/QCDB.md#global-tracking-data-request-helper)
+    * [Local CCDB setup](doc/QCDB.md#local-ccdb-setup)
+* [FLP Suite](doc/FLPsuite.md)
+    * [Developing QC modules on a machine with FLP suite](doc/FLPsuite.md#developing-qc-modules-on-a-machine-with-flp-suite)
+    * [Switch detector in the workflow <em>readout-dataflow</em>](doc/FLPsuite.md#switch-detector-in-the-workflow-readout-dataflow)
+    * [Get all the task output to the infologger](doc/FLPsuite.md#get-all-the-task-output-to-the-infologger)
+    * [Using a different config file with the general QC](doc/FLPsuite.md#using-a-different-config-file-with-the-general-qc)
+    * [Enable the repo cleaner](doc/FLPsuite.md#enable-the-repo-cleaner)
+    * [Reference data](doc/FLPsuite.md#reference-data)
+* [Miscellaneous](doc/Miscellaneous.md)
+    * [Asynchronous Data and Monte Carlo QC operations](doc/Miscellaneous.md#asynchronous-data-and-monte-carlo-qc-operations)
+    * [QCG](doc/Miscellaneous.md#qcg)
+    * [Data Sampling monitoring](doc/Miscellaneous.md#data-sampling-monitoring)
+    * [Monitoring metrics](doc/Miscellaneous.md#monitoring-metrics)
+    * [Common check IncreasingEntries](doc/Miscellaneous.md#common-check-increasingentries)
+    * [Common check TrendCheck](doc/Miscellaneous.md#common-check-trendcheck)
+    * [Update the shmem segment size of a detector](doc/Miscellaneous.md#update-the-shmem-segment-size-of-a-detector)
+    * [Readout chain](doc/Miscellaneous.md#readout-chain)
+    * [Writing a DPL data producer](doc/Miscellaneous.md#writing-a-dpl-data-producer)
 
 ### Where to get help