Update release notes and fix gears title

docs/pipelines/gears.md

-# Flexiprep
+# Gears
 
 ## Introduction
 Gears is a metagenomics pipeline. (``GE``nome ``A``nnotation of ``R``esidual ``S``equences). One can use this pipeline to identify contamination in sequencing runs on either raw FastQ files or BAM files.

docs/releasenotes/release_notes_0.5.0.md

 # Release notes Biopet version 0.5.0
 
-* Our QC and mapping pipeline now use piping for the most used aligners and QC tools
- * This decreases the disk usage and run time
-* Improvements in the reporting framework
-* Added metagenomics pipeline: [Gears](../pipelines/gears.md)
-* Development envoirment within the LUMC now get tested with Jenkins
- * Added integration tests Flexiprep
- * Added integration tests Mapping
- * Added integration tests Shiva
- * Added integration tests Toucan
+## General Code changes
+
+* Upgrade to Queue 3.4, with this also the htsjdk library to 1.132
+* Our `QC` and `Mapping` pipeline now use piping for the most used aligners and QC tools
+    * Reducing I/O over the network
+    * Reducing the disk usage (storage) and run time
 * Added version command for Star
+* Seperation of the `biopet`-framework into: `Core`, `Extensions`, `Tools` and `Utils`
+* Optimized unit testing
+* Unit test coverage on `Tools` increased
+* Workaround: Added R-script files of Picard to biopet to fix picard jobs (files are not packaged in maven dependency)
+* Added external example for developers
+
+## Functionality
+
+* Retries of pipeline and tools is now enabled by default
+* Improvements in the reporting framework, allowing custom reporting elements for specific pipelines.
+* Fixed reports when metrics of Flexiprep is skipped
+* Added metagenomics pipeline: [Gears](../pipelines/gears.md)
 * Added single sample variantcalling with bcftools
-* Splitting the Framework into: Core, Extensions, Tools and Utils
-* Fixed reports when Metrics of Flexiprep is skipped
-* Upgrade to Queue 3.4, with this also the htsjdk library to 1.132
-* Added key support for GATK jobs
-* Optimizing unit testing
-* Unit test coverage on Tools increased
-* Retry is now default enabled
+* Added ET + key support for GATK job invocation, disable phone-home feature when key is supplied
 * Added more debug information in the `.log` directory when `-l debug` is enabled
-* Shiva: added support for GenotypeConcordance tool to check against a Golden Standard
-* Workaround: Added Rscript files of picard to biopet to fix picard jobs (files are not packaged in maven dependency)
-* Shiva: fixed a lot of small bugs when developing integration tests
-* Gentrap: Better error handeling on missing annotation files
-* Shiva: Workaround: Fixed a dependency on rerun, with this change there can be 2 bam files in the samples folder
-* Added external example for developers
+* [Shiva](../pipelines/shiva.md): added support for `GenotypeConcordance` tool to check against a Golden Standard
+* [Shiva](../pipelines/shiva.md): fixed a lot of small bugs when developing integration tests
+* [Shiva](../pipelines/shiva.md): Workaround: Fixed a dependency on rerun, with this change there can be 2 bam files in the samples folder
+* [Gentrap](../pipelines/gentrap.md): Improved error handling on missing annotation files
+
+## Infrastructure changes
+
+* Development environment within the LUMC now get tested with Jenkins
+    * Added integration tests Flexiprep
+    * Added integration tests Gears
+    * Added integration tests Mapping
+    * Added integration tests Shiva
+    * Added integration tests Toucan