diff --git a/README.md b/README.md
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--- a/README.md
+++ b/README.md
@@ -6,62 +6,6 @@ Merge requests are welcome - if you find an issue, [please report to us](issues/
Compatible with: ShareLaTeX, pdfLaTeX, LuaLaTeX, XeLaTeX, LyX, latexmk.
-<div align=center>
+## Documentation
-
-
-</div>
-
-## Main menu
-
- * [Docker build environment](web/docker.md): read this if you want to generate
- the document locally using Docker or use a Git service (Gitlab / Github)
- for CI/CD.
-
- * [LaTeX virtual machine](web/vm.md): read this if you want to write the
- document locally using the preconfigured virtual machine (VM) or
- USB distribution provided by the Department of Future Technologies.
- The distribution provides: Debian stable, TeX Live, LyX, Pandoc,
- TeX editors, Emacs, Vim, Pygments, Seafile, Chromium, Docker.
-
- * [Using UTU ShareLaTeX](web/sharelatex.md): read this if you want to write
- the document in the cloud using the real-time collaborative ShareLaTeX
- service hosted by University of Turku.
-
- * [Using the thesis template](web/config.md): **you should read this**.
- Contains information on using and setting up the template.
-
- * [PDF/A configuration](web/pdfa.md): **you should read this**.
- Contains information on configuring the PDF/A settings.
-
-
-
-## Extra features
-
-- Should a required package be missing, see http://www.ctan.org/
-- Consultation of the manuals of these packages is strongly encouraged
-
-### R and LaTeX
-
-- https://www.tidyverse.org/
-- https://ggplot2.tidyverse.org/
-- https://yihui.name/knitr/
-- https://joshldavis.com/2014/04/12/beginners-tutorial-for-knitr/
-- https://gitlab.utu.fi/jmjmak/knitr-examples
-
-### Tools for benchmarking
-
-- https://github.com/sharkdp/hyperfine
-- https://github.com/Gabriel439/bench
-
-### Including source code
-
-- https://ctan.org/pkg/minted (preferred)
-- https://ctan.org/pkg/listingsutf8 (does not support full unicode)
-- https://ctan.org/pkg/sverb (still relevant?)
-
-## Miscellaneous
-
-- Report bugs via https://gitlab.utu.fi/ttweb/thesis/issues
-- LaTeX tutorial: http://www.ctan.org/tex-archive/info/lshort/english/lshort.pdf
-- Overleaf tutorials: https://www.overleaf.com/learn/latex/Tutorials
+**<https://ttweb.utugit.fi/thesis/doc/overview/>**
diff --git a/web/config.md b/web/config.md
deleted file mode 100644
index 503de64bf78b368ad874abfd785fa65c6bfa811f..0000000000000000000000000000000000000000
--- a/web/config.md
+++ /dev/null
@@ -1,253 +0,0 @@
-
-# Using the thesis template
-
-## Structure
-
-You're free to organize the project as you wish. A sane default structure
-looks like this:
-
- - root
- - `.gitlab-ci.yml`: configures CI/CD
- - `.gitignore`: configures git to ignore temp files
- - `utuftthesis.clss`: document class description
- - `thesis.xmpdata`: metadata for PDF/A generation
- - `latexmkrc`: build instructions for latexmk
- - `thesis.tex`: main document (links to sub-documents)
- - `bibliography.bib`: biblioraphy data (multiple bibs also possible)
- - `section-X.tex`: sub-documents for sections
- - `images/`: embedded images
- - `sources/`: embedded source code listings
-
-In case you're using LyX, the following extra files are needed (the tex
-files can be generated from the lyx files):
-
- - root
- - `utuftthesis.layout`: document class configuration for LyX
- - `thesis.lyx`: main document (links to sub-documents)
- - `section-X.lyx`: sub-documents for sections
-
-The standard files included in the template consist of:
-
-- The `latex` directory contains the document root. Everything from
- this directory can be moved to the project root, but make sure you'll
- update the GitLab CI, too.
-- The `tests` directory can be deleted. It contains an extensive test
- suite for the template.
-- The `web` directory can be deleted. It contains this documentation.
-- The document class file `utuftthesis.cls` is always required.
-- The `*.lyx` and `*.layout` files are only needed if you decide to
- use [LyX](https://www.lyx.org/), and can be deleted in other cases.
-
-## Workflow
-
-The documents are typically edited with
- - TeX editors
- - generic editors
- - LyX
- - hosted cloud services ([ShareLaTeX, Overleaf](sharelatex.md), or even GitLab Web IDE)
-
-The documents are compiled with
- - TeX → directly with TeX utilities (pdflatex/xelatex/tectonic) → PDF
- - TeX → LaTeX frontend (mklatex, arara etc.) → PDF
- - LyX → TeX → one of the previous two → PDF
- - LyX → PDF
- - [Integrated build system (ShareLaTeX / Overleaf) → PDF](sharelatex.md)
- - [CI/CD pipeline (GitLab) → PDF artifact / publish site](docker.md#setting-up-gitlab-cicd)
-
-Note that when using TeX utilities directly, you need to make sure the
-document has been fully processed. Usually this requires multiple
-compilation passes, interleaved with invocations of the auxiliary tools
-(glossary & bibliography generation etc.). Using the LaTeX frontend
-tools (latexmk) instead are highly recommended.
-
-## Document class configuration
-
-The thesis document class is described in [`utuftthesis.cls`](latex/utuftthesis.cls).
-
-- Based on the standard LaTeX `report` class
-- Proper page sizes as required by university guide for students:
- - proper font sizes as well as linespacings
- - proper size of margins
-- Document parameters (command: `\documentclass[the,parameters]{utuftthesis}`)
- - `version`: `draft` / `final` (default: `draft`) shows/hides [draft] in the footer
- - `language`: `finnish` / `english` (default: `finnish`) defines the main document
- language, affects the general document appearance and hyphenation
- - `mainfont`: (default: `times`)
- - pdftex: main font package (`lmodern`, `fourier`, ...), special value: `times`, `none`
- - xetex: main font name (Arial, Comic Sans, ...), special value: `times` enables Times New Roman, `none`
- - note: use `none` in cloud/CI services in place of `times` unless you provide the
- fonts yourself. The copyrighted fonts cannot be included in free platform
- distributions due to licensing issues.
- - `hidechapters`: `true` / `false` (default: `true`) hides/shows the chapter/luku
- text at the beginning of each Chapter
- - `countbibpages`: `true` / `false` (default: `false`) include bibliography
- pages when calculating the total number of pages
- - `sharelatex`: `true` / `false` (default: `false`) don't attempt to locate
- copyright protected system fonts, instead read them from the project
- repository
- - `emptyfirstpages`: `true` / `false` (default: `true`) clear the headers/footers
- for the 1st pages of text chapters
-- Extra document parameters (command: `\documentclass[extra,parameters]{utuftthesis}`)
- - `paper`: (default: `a4paper`) paper size
- - `pagecountdelta`: any integer (default: `-1`). Adjust the counting of app. pages
- - `pdfaconformance`: `a-1b`/ `a-2b` / `a-2u` / `a-3b` / `a-3u` / `none`
- (default: `a-2b`) PDF/A conformance level. A special parameter `mathxmp` can be
- also appended (see the PDF/A documentation).
- - `hidelinks`: `true` / `false` (default: `true`) hide the underlining of links
- - `minted`: `true` / `false` (default: `false`) use minted instead of listings
- for embedded code listings. Note that minted requires the use of `-shell-escape`
- build parameter.
- - `biburlbreak`: `ragged` / `split` / `none` (default: `split`) how to handle
- long urls in the bibliography
-- Publication metadata
- - `\pubyear{2000}`: the year of the publication
- - `\pubmonth{6}`: the month of the publication
- - `\publab{labname}`: the name of the laboratory, e.g. tietojenkäsittely
- - `\publaben{labname}`: the name of the laboratory in english, e.g. computer science
- - `\pubtype{type}`: the type of the thesis, special type name (`tkk`,
- `luk`, `gradu`, `di`), or a custom string for both fi/en
- - `\title{titlename}`: the title of the publication
- - `\author{authorname}`: the author of the publication
-- Abstract
- - `\abstract{text}`: abstract written in the main document language
- - `\abstracten{text}`: abstract written in english
- - `\keywords{kw1,kw2}`: list of keywords in the main document language
- - `\keywordsen{kw1,kw2}`: list of keywords in english
-- Title page
- - `\maketitle`: the standard LaTeX command for creating a title page. This template
- also creates the pages for abstracts
-- TOC and lists
- - `\tableofcontents`: generates the table of contents
- - `\listoffigures`: generates the list of figures
- - `\listoftables`: generates the list of tables
- - `\listofacronyms`: generates the list of acronyms (using the `nomencl` package)
-- Main content
- - `\begin{document}`: begins the main content
- - `\end{document}`: ends the main content
- - `\chapter{name}`: generates a new chapter (1)
- - `\section{name}`: generates a new section (1.1)
- - `\subsection{name}`: generates a new section (1.1.1)
- - `\printbibliography`: generates the bibliography list
- (required even if no bibliography has been used!)
- - `\appchapter{name}`: generates a new appendix chapter (A) after the bibliography list
-- Entry environment:
- - the actual items are aligned to suit the widest label, which is
- given as an argument to the environment
-```
-\begin{entry}[widest label]
- \item[1st label text] ...
- \item[2nd label text] ...
-\end{entry}
-```
-
-## PDF/A conformance and metadata
-
-The PDF/A generation mechanism is described in more detail in the
-[pdfx manual](ftp://ftp.funet.fi/pub/TeX/CTAN/macros/latex/contrib/pdfx/pdfx.pdf).
-
-### Configuration
-
-- First, compile the document using `version=final` in the document class parameters
-- The PDF/A conformance level can be configured with the `pdfaconformance` parameter
-- The default conformance level is `a-2b` (*PDF/A-2b: PDF/A-2b – Level B (basic) conformance*)
- - other supported values: `a-1b`, `a-2u`, `a-3b`, `a-3u`, `a-1a`, `a-2a`, `a-3a`, and `none`
- - the values `a-1a`, `a-2a`, and `a-3a` are still marked as experimental
- - the default conformance level should be sufficient for most thesis documents
- - `none` disables pdfx
-
-### Metadata file
-
-- The pdfx package explicitly disables the propagation of document metadata
- from the LaTeX preamble to PDF metadata fields (such aspdfauthor, pdftitle,
- pdfsubject, pdfkeywords, etc.). This should not be altered with hyperref
- as all the embedded metadata must be synchronized in conformant PDF/A
- documents.
-- Instead, the embedded PDF/A metadata is provided in XMP format and read from
- `<maindoc>.xmpdata` (just replace `<maindoc>` here with the main tex file,
- e.g. `thesis`).
-- For detailed documentation of the metadata fields and the process, please
- refer to the pdfx.pdf sections 2.2--2.3.
-- The following code ([`thesis.xmpdata`](latex/thesis.xmpdata)) is provided as an example:
-```
-\Title{Baking through the ages}
-\Author{A. Baker\sep C. Kneader}
-\Language{en-GB}
-\Keywords{cookies\sep muffins\sep cakes}
-\Publisher{University of Turku}
-```
-
-## Using the template
-
-### Git
-
-Start by cloning the whole template repository (or fork the project
-in GitLab).
-The following command line instructions can be used for setting up
-a new thesis (replace MYNAME with your utu username):
-
-```bash
-$ git clone https://gitlab.utu.fi/ttweb/thesis
-$ cd thesis
-$ git remote add mythesis https://gitlab.utu.fi/MYNAME/mythesis
-$ git push -u mythesis master
-```
-
-If you'd like to use the GitLab CI script, considering setting up
-the simplified CI pipeline that does not run the full test suite
-(invoke these commands in the thesis/ directory):
-
-```bash
-$ cp .gitlab-ci-simple.yml .gitlab-ci.yml
-$ rm -fr tests
-$ git add -A
-$ git ci -m 'Removed unnecessary testing.'
-$ git push
-```
-
-Changes to the project will be pushed to your `mythesis` repository
-(invoke these commands in the thesis/ directory):
-
-```bash
-$ touch test
-$ git add test
-$ git ci -m 'Just testing'
-$ git remote -v
-$ git push
-```
-
-### Latexmk (PdfTeX)
-
-PdfTeX is the default engine for compiling the template. It offers
-better compatibility with most features.
-
-When using latexmk, the project can be compiled like so:
-
-```bash
-$ latexmk -pdf -shell-escape thesis.tex
-```
-
-### Latexmk (XeTeX)
-
-XeTeX / XeLaTeX version is required if you want to use
-OpenType/TrueType fonts.
-
-When using latexmk, XeLaTeX version can be compiled like so:
-
-```bash
-$ latexmk -xelatex -shell-escape thesis.tex
-```
-
-### LyX
-
-LyX provides a graphical WYSIWYM interface for editing TeX-like
-LyX documents that can be converted to TeX. The template distribution
-contains the `utuftthesis.layout` document class description file
-for the same `utuftthesis.cls` as the one used by TeX documents.
-
-Start by editing the provided `thesis.lyx`. The file has been configured
-to use the custom `utuftthesis` document class.
-
-Depending on your LyX version, you may need to enable `-shell-escape`
-from the global LyX settings. Follow the program's instructions.
-When updating your TeX distribution, LyX may require reconfiguration.
-This functionality is available via the tools menu.
diff --git a/web/docker.md b/web/docker.md
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--- a/web/docker.md
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-
-# Docker build environment
-
-A custom LaTeX build environment based on *Debian stable* has been developed
-using *Docker* based container technologies. The purpose of this container
-is to facilitate LaTeX document generation using GitLab CI/CD pipelines. The
-same image can also be used for generating documents either using the standard
-command line prompt or as a backend for new middleware.
-
-The container's TeX distribution is based on
-[TinyTeX](https://yihui.org/tinytex/) + TeX 'small' scheme + additional
-packages. See the [`Dockerfile`](Dockerfile) for a full list of installed
-TeX packages. In addition, a headless Java JRE is provided for
-[VeraPDF](https://verapdf.org/) powered [PDF/A validation](pdfa.md), poppler utils
-for analyzing the generated PDF files (`pdfinfo`, `pdffonts` etc.), and
-python3 + pygments for pretty printing source code using the LaTeX
-[minted](https://ctan.org/pkg/minted) package.
-
-Docker image available at Docker Hub: https://hub.docker.com/repository/docker/konttipoju/tinytex
-
-
-## Setting up GitLab CI/CD
-
-The project's [GitLab CI script](.gitlab-ci.yml) provides an rather complex
-example of using the Docker image in GitLab in various ways (building documents,
-asserting certain properties, validating PDF/A conformance).
-
-[This simplified version](.gitlab-ci-simple.yml) can be used instead:
-
-```yaml
-# see https://hub.docker.com/repository/docker/konttipoju/tinytex
-image: konttipoju/tinytex:2020-04a
-
-# build latex/thesis.tex -> latex/thesis.pdf using pdflatex
-# shell-escape functionality is required by the minted package
-build:
- stage: build
- script:
- - cd latex
- - latexmk -pdf --shell-escape thesis.tex
- artifacts:
- paths:
- - latex/thesis.pdf
-
-# a validation prints "PASS + something" is the file is PDF/A conformant
-validate:
- stage: test
- script:
- - pdfa-validate latex/thesis.pdf|grep '^PASS'
-```
-
-You're also free to consider other LaTeX Docker images such as these:
- * https://github.com/blang/latex-docker
- * https://github.com/natlownes/docker-latex
-
-
-## Installing new TeX packages
-
-If a certain package is missing, the Dockerfile can be modified, but adding few
-extra packages is even simpler by just invoking `tlmgr`:
-
-```bash
-$ tlmgr install packagename
-```
-
-The packages can be installed even inside the CI script. However, in case the
-document will be recompiled multiple times, generating a new Docker image and
-caching it locally is recommended. Otherwise the public repositories might
-block access to fight the bandwidth costs.
-
-### Validating PDF/A conformance
-
-A headless Java 11 JRE is provided in the Docker image for VeraPDF powered
-PDF/A validation:
-
-```bash
-$ pdfa-validate thesis.pdf
-```
-
-See the [PDF/A page](web/pdfa.md) for further instructions.
-
-## Compiling the thesis using Docker
-
-We assume the thesis is located in the local folder `thesis/`. The currently
-active user also needs to belong in the 'docker' group. Otherwise try
-`sudo docker` in place of plain `docker`. In addition, the Docker
-service needs to be active (try `systemctl start docker`).
-
-The build environment first needs to be fetched from Docker Hub:
-
-```bash
-$ docker pull konttipoju/tinytex:2020-04a
-```
-
-We can then list all the available container images:
-```bash
-$ docker images
-REPOSITORY TAG IMAGE ID CREATED SIZE
-konttipoju/tinytex 2020-04a 4e7da92afcfa 2 hours ago 765MB
-debian buster-slim 2dbffcb4f093 4 weeks ago 69.2MB
-```
-
-An interactive shell can be launched in the LaTeX container. This shell
-provides access to compile the thesis:
-
-```
-$ docker container run -it --mount type=bind,source=$(pwd)/thesis,target=/thesis 4e7da92afcfa /bin/bash
-root@d662b10721e7:/var/local# cd /thesis
-root@d662b10721e7:/tex# latexmk -pdf --shell-escape thesis.tex
-```
-
-The results of the compilation will be available in the `thesis/` directory.
-In case the compilation succeeds and the document was compiled in the `final`,
-not `draft` mode, the resulting `thesis.pdf` should be a PDF/A conformant
-final version.
diff --git a/web/overleaf.png b/web/overleaf.png
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-
-# PDF/A conformance and metadata
-
-The PDF/A generation mechanism is described in more detail in the
-[pdfx manual](ftp://ftp.funet.fi/pub/TeX/CTAN/macros/latex/contrib/pdfx/pdfx.pdf).
-
-## Configuration
-
-- First, compile the document using `version=final` in the document class parameters
-- The PDF/A conformance level can be configured with the `pdfaconformance` parameter
-- The default conformance level is `a-2b` (*PDF/A-2b: PDF/A-2b – Level B (basic) conformance*)
- - other supported values: `a-1b`, `a-2u`, `a-3b`, `a-3u`, `a-1a`, `a-2a`, `a-3a`, and `none`
- - the values `a-1a`, `a-2a`, and `a-3a` are still marked as experimental
- - the default conformance level should be sufficient for most thesis documents
- - `none` disables pdfx
-
-## Metadata file (thesis.xmpdata)
-
-- The pdfx package explicitly disables the propagation of document metadata
- from the LaTeX preamble to PDF metadata fields (such aspdfauthor, pdftitle,
- pdfsubject, pdfkeywords, etc.). This should not be altered with hyperref
- as all the embedded metadata must be synchronized in conformant PDF/A
- documents.
-- Instead, the embedded PDF/A metadata is provided in XMP format and read from
- `<maindoc>.xmpdata` (just replace `<maindoc>` here with the main tex file,
- e.g. `thesis`).
-- For detailed documentation of the metadata fields and the process, please
- refer to the pdfx.pdf sections 2.2--2.3.
-- The following code (`thesis.xmpdata`) is provided as an example:
-```
-\Title{Baking through the ages}
-\Author{A. Baker\sep C. Kneader}
-\Language{en-GB}
-\Keywords{cookies\sep muffins\sep cakes}
-\Publisher{University of Turku}
-```
-
-## Tools
-
-Note that PDF/A support is a rather new feature in LaTeX, e.g. the pdfx
-1.6.3 library was announced 2019/2/27. If the document fails to validate,
-consider compiling with a more recent LaTeX distribution. The template
-has been tested with TeXLive 2017+.
-
-### VeraPDF (generic instructions)
-
-A free [VeraPDF](https://verapdf.org/) tool can be used to test if the
-resulting PDF files are PDF/A conformant. Unfortunately, the official
-VeraPDF distribution may not build. Use the snapshot
-[version hosted at UTU gitlab](https://gitlab.utu.fi/jmjmak/veraPDF-apps)
-instead.
-
-The following script shows how to invoke the VeraPDF tool:
-
-```bash
-$ wget https://gitlab.utu.fi/jmjmak/veraPDF-apps/raw/integration/greenfield-apps-1.15.0-SNAPSHOT.jar?inline=false -O validator.jar
-$ latexmk -pdf -shell-escape thesis.tex
-$ java -cp validator.jar org.verapdf.apps.GreenfieldCliWrapper --format text -v thesis.pdf
-```
-
-### VeraPDF (Docker image)
-
-A headless Java 11 JRE is provided in the Docker image for VeraPDF
-powered PDF/A validation. The UTU build of the VeraPDF tool is also
-included in the [LaTeX Docker image](web/docker.md) and can be run by
-simply invoking:
-
-```bash
-$ pdfa-validate thesis.pdf
-```
-
-The [GitLab CI script](.gitlab-ci-simple.yml)
-in this project demonstrates the validation of CI/CD generated PDFs with
-this tool.
-
-## Limitations
-
-- pdfTeX should not have any significant limitations
-- luaLaTeX expects all input documents to be encoded using utf-8 (mainly
- a problem for Windows users)
-- XeLaTeX generated documents may fail when using OTF fonts (see the
- [pdfx manual](ftp://ftp.funet.fi/pub/TeX/CTAN/macros/latex/contrib/pdfx/pdfx.pdf)
- section 3.1.1).
-- XeLaTeX requires the extra parameter (`-output-driver="xdvipdfmx -z 0"`)
- which is included in the provided `latexmkrc`.
-- XeLaTeX will not generate conforming PDF/A documents when the
- output-directory is changed in `latexmk`.
-- Configuring a default action (hyperref) when opening the PDF will
- produce non-conforming PDF files.
-
-## What are these PDF/A conformance rules?
-
-The VeraPDF page contains a list of validation rules:
-
- * https://github.com/veraPDF/veraPDF-validation-profiles/wiki/PDFA-Part-1-rules
- * https://github.com/veraPDF/veraPDF-validation-profiles/wiki/PDFA-Parts-2-and-3-rules
-
-Related:
- * https://utuguides.fi/opinnayte/pdfa
- * https://coursepages.uta.fi/mtta1-latex/pdf-a/
diff --git a/web/sharelatex.md b/web/sharelatex.md
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-# Setting up ShareLaTeX
-
-A ShareLaTeX platform is hosted on-premises at UTU Software Engineering Laboratory: https://tex.soft.utu.fi/
-
-Press register at the top right corner to register for the service.
-
-See the general LaTeX document guide for configuring the template.
-
-The following set of screenshots describes the process of exporting the
-thesis template from the GitLab to ShareLaTeX (exporting to Overleaf
-differs slightly, but this instruction can be applied):
-
-## Step 1: export the project
-
-<div align=center>
-
-
-
-</div>
-
-## Step 2: store the zip file locally
-
-<div align=center>
-
-
-
-</div>
-
-
-## Step 3: create a new ShareLaTeX project
-
-<div align=center>
-
-
-
-</div>
-
-
-## Step 4: use the zip (step 2) as project template
-
-<div align=center>
-
-
-
-
-
-</div>
-
-
-## Step 5: delete the tests folder
-
-<div align=center>
-
-
-
-</div>
-
-
-## Step 6: set up the main TeX document
-
-<div align=center>
-
-
-
-
-</div>
-
-
-## Step 7: recompile using the new main document
-
-<div align=center>
-
-
-
-</div>
-
-
-## Done
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-
-# LaTeX virtual machine
-
-The Department of Future Technologies provides a set of virtual machines for
-software development and other tasks via https://ftdev.utu.fi/. The `utuvm-latex`
-virtual machine is especially preconfigured for generating LaTeX documents.
-The virtual machine has been tested to build this document template without
-any issues.
-
-The `utuvm-latex` virtual machine contains preinstalled versions of
- * TeX Live (popular Linux/Unix LaTeX distribution)
- * LyX (for WYSIWYM editing)
- * Pandoc for generating LaTeX documents from markdown sources
- * TeX editors (Gummy, Texworks, Texmaker, Texstudio)
- * Generic editors (Emacs, Vim, Geany, nano)
- * PDF reader (Evince)
- * Pygments for syntax highlighting (minted)
- * Seafile client for storing the documents in the University's
- Seafile server.
- * [Docker](docker.md#compiling-the-thesis-using-docker), systemd-nspawn
-
-The virtual machine also comes with a modern browser (Chromium) for editing
-documents in ShareLaTeX and Overleaf.
-
-Extra applications can be easily installed from deb packages.
-
-
-
-## Using the virtual machine
-
-Please refer to the instructions on the virtual machine site for
-setting up the platform.
-
-The TeX tools in the VM are standard without further customizations.
-The [general instructions on using the template](web/config.md)
-should cover the usage of the provided tools.
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