Minor edits to various parts

Some edits were made after rereading of some parts.

2 files changed, 54 insertions, 17 deletions

diff --git a/tex/src/figure-file-architecture.tex b/tex/src/figure-file-architecture.tex
index a4d4755..e08ee52 100644
--- a/tex/src/figure-file-architecture.tex
+++ b/tex/src/figure-file-architecture.tex
@@ -10,7 +10,7 @@
   \footnotesize
 
   %% project/
-  \node [dirbox, at={(0,4cm)}, minimum width=15cm, minimum height=9cm,
+  \node [dirbox, at={(0,4cm)}, minimum width=15cm, minimum height=9.9cm,
     label={[shift={(0,-5mm)}]\texttt{project/}}] {};
   \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-6.0cm,3.3cm)}] {COPYING};
@@ -31,7 +31,7 @@
   \node [dirbox, at={(-4.35cm,2.1cm)}, minimum width=5.7cm, minimum height=5.3cm,
     label={[shift={(0,-5mm)}]\texttt{software/}}, fill=brown!20!white] {};
 
-  %% reproduce/software/config
+  %% reproduce/software/config/
   \node [dirbox, at={(-5.75cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
     label={[shift={(0,-5mm)}]\texttt{config/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
@@ -42,7 +42,7 @@
   \node [node-nonterminal-thin, at={(-5.75cm,-0.2cm)}] {checksums.conf};
   \fi
 
-  %% reproduce/software/make
+  %% reproduce/software/make/
   \node [dirbox, at={(-2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
     label={[shift={(0,-5mm)}]\texttt{make/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
@@ -53,15 +53,15 @@
   \node [node-nonterminal-thin, at={(-2.95cm,-0.2cm)}] {python.mk};
   \fi
 
-  %% reproduce/software/bash
+  %% reproduce/software/bash/
   \node [dirbox, at={(-5.75cm,-0.8cm)}, minimum width=2.6cm, minimum height=1.6cm,
-    label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {};
+    label={[shift={(0,-5mm)}]\texttt{shell/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
-  \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {bashrc.sh};
-  \node [node-nonterminal-thin, at={(-5.75cm,-2.0cm)}] {configure.sh};
+  \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {configure.sh};
+  \node [node-nonterminal-thin, at={(-5.75cm,-2.0cm)}] {bashrc.sh};
   \fi
 
-  %% reproduce/software/bibtex
+  %% reproduce/software/bibtex/
   \node [dirbox, at={(-2.95cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
     label={[shift={(0,-5mm)}]\texttt{bibtex/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
@@ -74,7 +74,7 @@
   \node [dirbox, at={(1.55cm,2.1cm)}, minimum width=5.7cm, minimum height=5.3cm,
     label={[shift={(0,-5mm)}]\texttt{analysis/}}, fill=brown!20!white] {};
 
-  %% reproduce/analysis/config
+  %% reproduce/analysis/config/
   \node [dirbox, at={(0.15cm,1.5cm)}, minimum width=2.6cm, minimum height=2.6cm,
     label={[shift={(0,-5mm)}]\texttt{config/}}, fill=brown!25!white] {};
   \node [node-nonterminal-thin, at={(0.15cm,0.8cm)}] {INPUTS.conf};
@@ -82,7 +82,7 @@
   \node [node-nonterminal-thin, at={(0.15cm,-0.2cm)}] {param-2a.conf};
   \node [node-nonterminal-thin, at={(0.15cm,-0.7cm)}] {param-2b.conf};
 
-  %% reproduce/analysis/make
+  %% reproduce/analysis/make/
   \node [dirbox, at={(2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.6cm,
     label={[shift={(0,-5mm)}]\texttt{make/}}, fill=brown!25!white] {};
   \node [node-nonterminal-thin, at={(2.95cm,0.8cm)}] {top-prepare.mk};
@@ -90,14 +90,14 @@
   \node [node-nonterminal-thin, at={(2.95cm,-0.2cm)}] {initialize.mk};
   \node [node-nonterminal-thin, at={(2.95cm,-0.7cm)}] {analysis1.mk};
 
-  %% reproduce/analysis/bash
+  %% reproduce/analysis/bash/
   \node [dirbox, at={(0.15cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.1cm,
     label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(0.15cm,-2.0cm)}] {process-A.sh};
   \fi
 
-  %% reproduce/analysis/python
+  %% reproduce/analysis/python/
   \node [dirbox, at={(2.95cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{python/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
@@ -109,7 +109,7 @@
   \node [dirbox, at={(6cm,2.6cm)}, minimum width=2.7cm, minimum height=6cm,
     label={[shift={(0,-5mm)}]\texttt{tex/}}, fill=brown!15!white] {};
 
-  %% tex/src
+  %% tex/src/
   \node [dirbox, at={(6cm,2.1cm)}, minimum width=2.5cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{src/}}, fill=brown!20!white] {};
   \node [node-nonterminal-thin, at={(6cm,1.4cm)}] {references.tex};
@@ -117,7 +117,7 @@
   \node [node-nonterminal-thin, at={(6cm,0.9cm)}] {figure-1.tex};
   \fi
 
-  %% tex/build
+  %% tex/build/
   \ifdefined\fullfilearchitecture
   \node [dirbox, at={(6cm,0.1cm)}, minimum width=2.5cm, minimum height=1.3cm,
     label={[shift={(0,-5mm)}]\texttt{build/}}, dashed, , fill=brown!20!white] {};
@@ -125,7 +125,7 @@
   \node [anchor=west, at={(4.7cm,-1.0cm)}] {\scriptsize\sf \LaTeX{} build directory.};
   \fi
 
-  %% tex/tikz
+  %% tex/tikz/
   \ifdefined\fullfilearchitecture
   \node [dirbox, at={(6cm,-1.6cm)}, minimum width=2.5cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{tikz/}}, dashed, fill=brown!20!white] {};
@@ -134,7 +134,7 @@
   \node [anchor=west, at={(4.67cm,-3.0cm)}] {\scriptsize\sf by \LaTeX).};
   \fi
 
-  %% .local
+  %% .local/
   \ifdefined\fullfilearchitecture
   \node [dirbox, at={(-3.6cm,-3.6cm)}, minimum width=7cm, minimum height=1.2cm,
     label={[shift={(0,-5mm)}]\texttt{.local/}}, dashed, fill=brown!15!white] {};
@@ -144,7 +144,7 @@
         {\scriptsize\sf Python or R, run `\texttt{.local/bin/python}' or `\texttt{.local/bin/R}'};
   \fi
 
-  %% .build
+  %% .build/
   \ifdefined\fullfilearchitecture
   \node [dirbox, at={(3.6cm,-3.6cm)}, minimum width=7cm, minimum height=1.2cm,
     label={[shift={(0,-5mm)}]\texttt{.build/}}, dashed, fill=brown!15!white] {};
@@ -153,4 +153,13 @@
   \node [anchor=west, at={(0.1cm,-4.6cm)}]
         {\scriptsize\sf Enabling easy access to all of project's built components.};
   \fi
+
+  %% .git/
+  \ifdefined\fullfilearchitecture
+  \node [dirbox, at={(0,-5cm)}, minimum width=14.2cm, minimum height=7mm,
+    label={[shift={(0,-5mm)}]\texttt{.git/}}, dashed, fill=brown!15!white] {};
+  \node [anchor=north, at={(0cm,-5.3cm)}]
+        {\scriptsize\sf Full project temporal provenance (version controlled history) in Git.};
+  \fi
+
 \end{tikzpicture}
diff --git a/tex/src/references.tex b/tex/src/references.tex
index 68d59d3..305c3ab 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -35,6 +35,20 @@ archivePrefix = {arXiv},
 
 
 
+@ARTICLE{perignon19,
+     author = {Christophe P\'erignon and Kamel Gadouche and Christophe Hurlin and Roxane Silberman and Eric Debonnel},
+      title = {Certify reproducibility with confidential data},
+       year = {2019},
+    journal = {Science},
+     volume = {365},
+      pages = {127},
+        doi = {10.1126/science.aaw2825},
+}
+
+
+
+
+
 @ARTICLE{munafo19,
      author = {Marcus Munaf\'o},
       title = {Raising research quality will require collective action},
@@ -1537,6 +1551,20 @@ Reproducible Research in Image Processing},
 
 
 
+@ARTICLE{mcilroy78,
+     author = {M. D. McIlroy and E. N. Pinson and B. A. Tague},
+      title = {UNIX Time-Sharing System: Forward},
+    journal = {\doihref{https://archive.org/details/bstj57-6-1899/mode/2up}{Bell System Technical Journal}},
+       year = {1978},
+     volume = {57},
+      pages = {6, ark:/13960/t0gt6xf72},
+        doi = {},
+}
+
+
+
+
+
 @ARTICLE{anscombe73,
      author = {{Anscombe}, F.J.},
       title = {Graphs in Statistical Analysis},