Cleaned abstract and Section II to fit word limit

In the abstract the repeated benefits of Maneage (which are also mentioned
in the criteria) were removed to fit into CiSE's online submission
guidelines. In Section II (Longevity of existing tools), the paragraph that
itemized the following paragrahs as a numbered list has been removed with
the sentence that repeatedly states the importance of reproducibility in
the sciences and some branches of the industry.

With these changes our approximate automatic count has 6277 words. This is
still very slightly larger than the 6250 word limit of the
journal. However, this count is a definite over-estimation (including many
things like page titles and page numberings from the raw PDF to text
conversion). So the actual count for the journal publication should be less
than this.

A few other tiny corrections were made:

 - The year of the paper and copyright in 'README.md' was set to 2021. The
   copyright of the rest of the files will be set to 2021 after the next
   merge with Maneage soon (the years of core infrastructure copyrights has
   already been corrected there).

 - Mohammadreza's name was added in 'README.md'.

 - The line to import the "necessity" appendix has been commented in the
   version to have the full paper in one PDF (to be upladed to arXiv or
   Zenodo).

 - The supplement PDF now starts with '\appendices' so the sections have
   the same labels as the single-PDF version.

1 files changed, 11 insertions, 16 deletions

diff --git a/paper.tex b/paper.tex
index 778cb19..79503f2 100644
--- a/paper.tex
+++ b/paper.tex
@@ -72,12 +72,12 @@
   %% CONTEXT
   Analysis pipelines commonly use high-level technologies that are popular when created, but are unlikely to be readable, executable, or sustainable in the long term.
   %% AIM
-  A set of criteria is introduced to address this problem.
+  A set of criteria is introduced to address this problem:
   %% METHOD
   Completeness (no \new{execution requirement} beyond \new{a minimal Unix-like operating system}, no administrator privileges, no network connection, and storage primarily in plain text); modular design; minimal complexity; scalability; verifiable inputs and outputs; version control; linking analysis with narrative; and free software.
   They have been tested in several research publications in various fields.
   %% RESULTS
-  As a proof of concept, ``Maneage'' is introduced for storing projects in machine-actionable and human-readable plain text, enabling cheap archiving, provenance extraction, and peer verification.
+  As a proof of concept, ``Maneage'' is introduced, enabling cheap archiving, provenance extraction, and peer verification.
   %% CONCLUSION
   We show that longevity is a realistic requirement that does not sacrifice immediate or short-term reproducibility.
   The caveats (with proposed solutions) are then discussed and we conclude with the benefits for the various stakeholders.
@@ -85,15 +85,15 @@
 
   \vspace{2.5mm}
   \emph{Appendices} ---
-  Two comprehensive appendices that review existing solutions; available
+  Two comprehensive appendices that review the longevity of existing solutions; available
 \ifdefined\separatesupplement
-at \href{https://arxiv.org/abs/\projectarxivid}{\texttt{arXiv:\projectarxivid}} or \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}}.
+as supplementary ``Web extras'' on the journal webpage.
 \else
-at the end (Appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}).
+after main body of paper (Appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}).
 \fi
 
   \vspace{2.5mm}
-  \emph{Reproducible supplement} ---
+  \emph{Reproducibility} ---
   All products in \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{\texttt{zenodo.\projectzenodoid}},
   Git history of source at \href{https://gitlab.com/makhlaghi/maneage-paper}{\texttt{gitlab.com/makhlaghi/maneage-paper}},
   which is also archived in \href{https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/makhlaghi/maneage-paper.git}{SoftwareHeritage}.
@@ -147,19 +147,13 @@ Longevity is defined as the length of time that a project remains \emph{function
 Functionality is defined as \emph{human readability} of the source and its \emph{execution possibility} (when necessary).
 Many usage contexts of a project do not involve execution: for example, checking the configuration parameter of a single step of the analysis to re-\emph{use} in another project, or checking the version of used software, or the source of the input data.
 Extracting these from execution outputs is not always possible.}
-
-Longevity is as important in science as in some fields of industry, but not all; e.g., fast-evolving tools can be appropriate in short-term commercial projects.
-To highlight the necessity, a short review of commonly-used tools is provided below:
-(1) environment isolators (virtual machines, VMs, or containers);
-(2) package managers (PMs, like Conda, Nix, or Spack);
-(3) job management (like shell scripts or Make);
-(4) notebooks (like Jupyter).
-\new{A comprehensive review of existing tools and solutions is available in the
+A basic review of the longevity of commonly-used tools is provided here \new{(for a more comprehensive review, please see
   \ifdefined\separatesupplement
-  \href{https://doi.org/10.5281/zenodo.\projectzenodoid}{appendices}.%
+  the supplementary appendices%
   \else%
-  appendices (\ref{appendix:existingsolutions}).%
+  appendices \ref{appendix:existingtools} and \ref{appendix:existingsolutions}%
   \fi%
+  ).
 }
 
 To isolate the environment, VMs have sometimes been used, e.g., in \href{https://is.ieis.tue.nl/staff/pvgorp/share}{SHARE} (awarded second prize in the Elsevier Executable Paper Grand Challenge of 2011, but discontinued in 2019).
@@ -692,6 +686,7 @@ The Pozna\'n Supercomputing and Networking Center (PSNC) computational grant 314
 \input{tex/src/appendix-existing-tools.tex}
 \input{tex/src/appendix-existing-solutions.tex}
 \input{tex/src/appendix-used-software.tex}
+%\input{tex/src/appendix-necessity.tex}
 \bibliographystyleappendix{IEEEtran_openaccess}
 \bibliographyappendix{IEEEabrv,references}
 \fi