tidying up some recent changes

Author: nevrome

trident.md

@@ -880,7 +880,7 @@ Note that all three files, the source, the target, and the outfile, are mandator
 - `sourceFile` -> This is the file from which to read additional columns that might be missing in the target.
 - `outFile` -> This is the file that will contain the coalesced result.
 
-In addition to these three files, you can choose a Poseidon Version for both the source (`--pvSource`) and the target (`--pvTarget`), which is useful for backwards compatibility, in case you have Janno files in older Poseidon versions. **_But_**: Note that the output file will _always_ be written in the newest Poseidon version. Note that you _can_ choose the outFile to be the targetFile, which will then overwrite the target file. This can be useful if you know what you are doing. Otherwise it is of course safer to choose a new filename for the output. 
+In addition to these three files, you can choose a Poseidon Version for both the source (`--pvSource`) and the target (`--pvTarget`), which is useful for backwards compatibility, in case you have `.janno` files in older Poseidon versions. **_But_**: Note that the output file will _always_ be written in the newest Poseidon version. Note that you _can_ choose the outFile to be the targetFile, which will then overwrite the target file. This can be useful if you know what you are doing. Otherwise it is of course safer to choose a new filename for the output. 
 
 ## Rectify command
 

trident_guide_archive/.DS_Store

@@ -1,52 +1,3 @@
-<popup :custom-text="`<p><a href='https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024'>A short introduction to the Poseidon genotype data management framework</a> by Clemens Schmid: A Poseidon tutorial showcasing the <a href='https://nevrome.github.io/uni.tuebingen.poseidon.intro.2h.2024/ref_pca.html'>main features of trident</a> among other things</p>`"></popup>
-
-<h1>trident CLI software</h1>
-
-`trident` is a command line software tool to work with Poseidon packages and handle various data management tasks. It is written in Haskell and openly available on [GitHub](https://github.com/poseidon-framework/poseidon-hs/).
-
-[![CI](https://github.com/poseidon-framework/poseidon-hs/actions/workflows/main.yml/badge.svg?branch=master)](https://github.com/poseidon-framework/poseidon-hs/actions/workflows/main.yml)
-[![Coverage Status](https://img.shields.io/codecov/c/github/poseidon-framework/poseidon-hs/master.svg)](https://codecov.io/github/poseidon-framework/poseidon-hs?branch=master)
-[![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/poseidon-framework/poseidon-hs?include_prereleases) ![GitHub all releases](https://img.shields.io/github/downloads/poseidon-framework/poseidon-hs/total)](https://github.com/poseidon-framework/poseidon-hs/releases)
-[![Install with Bioconda](https://anaconda.org/bioconda/poseidon-trident/badges/version.svg)](https://anaconda.org/bioconda/poseidon-trident) [![Anaconda-Server Badge](https://anaconda.org/bioconda/poseidon-trident/badges/downloads.svg)](https://anaconda.org/bioconda/poseidon-trident)
-
-To download the latest stable release version of `trident` click here:
-[📥 Linux](https://github.com/poseidon-framework/poseidon-hs/releases/latest/download/trident-Linux) |
-[📥 macOS (ARM64)](https://github.com/poseidon-framework/poseidon-hs/releases/latest/download/trident-macOS-ARM64) |
-[📥 macOS (X64)](https://github.com/poseidon-framework/poseidon-hs/releases/latest/download/trident-macOS-X64) |
-[📥 Windows](https://github.com/poseidon-framework/poseidon-hs/releases/latest/download/trident-Windows.exe)
-
-So in Linux you can run the following commands to get started:
-
-```bash
-# download the current stable release binary
-wget https://github.com/poseidon-framework/poseidon-hs/releases/latest/download/trident-Linux
-# make it executable
-chmod +x trident-Linux
-# run it
-./trident-Linux -h
-```
-
-On GitHub you will also find [older release versions](https://github.com/poseidon-framework/poseidon-hs/releases) and [instructions to build `trident` from source](https://github.com/poseidon-framework/poseidon-hs#for-haskell-developers). The relevant changes from one version to the next are documented in this [changelog](https://github.com/poseidon-framework/poseidon-hs/blob/master/CHANGELOGRELEASE.md).
-
-With `trident --help` and `trident <subcommand> --help` you can get information about each subcommand and parameter directly on the command line. The guide below explains the subcommands in more detail. It is available in .pdf format for the current and previous versions here:
-
-- [🗎 Guide for trident v1.6.7.1 to v1.6.7.3](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident.pdf) (shown below)
-- [🗎 Guide for trident v1.6.2.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.6.2.1.pdf)
-- [🗎 Guide for trident v1.5.7.0 to v1.5.7.3](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.5.7.0_to_1.5.7.3.pdf)
-- [🗎 Guide for trident v1.5.4.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.5.4.0.pdf)
-- [🗎 Guide for trident v1.4.1.0 to v1.5.0.1](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.4.1.0_to_1.5.0.1.pdf)
-- [🗎 Guide for trident v1.4.0.2 to v1.4.0.3](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.4.0.2_to_1.4.0.3.pdf)
-- [🗎 Guide for trident v1.3.0.4](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.3.0.4.pdf)
-- [🗎 Guide for trident v1.2.0.0 to v1.2.1.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.2.0.0_to_1.2.1.0.pdf)
-- [🗎 Guide for trident v1.1.11.0 to v1.1.12.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.1.11.0_to_1.1.12.0.pdf)
-- [🗎 Guide for trident v1.1.10.2](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.1.10.2.pdf)
-- [🗎 Guide for trident v1.1.7.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.1.7.0.pdf)
-- [🗎 Guide for trident v1.1.6.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.1.6.0.pdf)
-- [🗎 Guide for trident v1.1.0.0 to v1.1.4.2](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.1.0.0_to_1.1.4.2.pdf)
-- [🗎 Guide for trident v1.0.0.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_1.0.0.0.pdf)
-- [🗎 Guide for trident v0.29.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_0.29.0.pdf)
-- [🗎 Guide for trident v0.28.0](https://github.com/poseidon-framework/poseidon-framework.github.io/blob/master/trident_guide_archive/trident_guide_0.28.0.pdf)
-
 # Guide for trident v1.6.7.1 to v1.6.7.3
 
 ## Installation