Sanity checks added, local settings now in LOCAL.mk.in

The choice of whether or not to make a PDF is now also a local system
issue, not a general pipeline issue. So it has been put in the new
`LOCAL.mk.in' file which replaces the old `DIRECTORIES.mk.in'. All local
settings (things that when changed should not be version-controlled) should
be defined in this file.

A sanity check was added to find if `./configure' has been run before
`make' or not (using the `LOCAL.mk' file which is an output of the
configuration step). If `LOCAL.mk' doesn't exist, an error will be printed
informing the user that `./configure' needs to be run first.

The configure script also provides more clear and hopefully better
information on its purpose and what must be done.

Since `make clean', it is executed even when `./configure' hasn't been run,
it will only delete the build directory and its contents when local
configuration has been done.

A `distclean' target was also added which will first "clean" the pipeline,
then delete the `LOCAL.mk.in' file.

To allow rules like `make' to be run even if `BDIR' isn't defined
(`./configure' hasn't been run yet), a fake `BDIR' is defined in such
cases.

1 files changed, 18 insertions, 18 deletions

diff --git a/README.md b/README.md
index 5f0d3e4..59ecf71 100644
--- a/README.md
+++ b/README.md
@@ -179,24 +179,24 @@ been explained here), please let us know to correct it.
 
  - **First input dataset**: The user manages the top-level directory of the
      input data through the variables set in
-     `reproduce/config/pipeline/DIRECTORIES.mk.in` (the user actually edits
-     a `DIRECTORIES.mk` file that is created by `configure` from the
-     `.mk.in` file, but the `.mk` file is not under version control). So
-     open this file and replace `SURVEY` in the variable name and value
-     with the name of your input survey or dataset (all in capital
-     letters), for example if you are working on data from the XDF survey,
-     replace `SURVEY` with `XDF`. Don't change anything else in the value,
-     just the the all-caps name. Afterwards, change any occurrence of
-     `SURVEY` in the whole pipeline with the new name. You can find the
-     occurrences with a simple command like the ones shown below. We follow
-     the Make convention here that all `ONLY-CAPITAL` variables are those
-     directly set by the user and all `small-caps` variables are set by the
-     pipeline designer. All variables that also depend on this survey have
-     a `survey` in their name. Hence, also correct all these occurrences to
-     your new name in small-caps. Of course, ignore those occurrences that
-     are irrelevant, like those in this file. Note that in the raw version
-     of this template no target depends on these files, so they are
-     ignored. Afterwards, set the webpage and correct the filenames in
+     `reproduce/config/pipeline/LOCAL.mk.in` (the user actually edits a
+     `LOCAL.mk` file that is created by `configure` from the `.mk.in` file,
+     but the `.mk` file is not under version control). So open this file
+     and replace `SURVEY` in the variable name and value with the name of
+     your input survey or dataset (all in capital letters), for example if
+     you are working on data from the XDF survey, replace `SURVEY` with
+     `XDF`. Don't change anything else in the value, just the the all-caps
+     name. Afterwards, change any occurrence of `SURVEY` in the whole
+     pipeline with the new name. You can find the occurrences with a simple
+     command like the ones shown below. We follow the Make convention here
+     that all `ONLY-CAPITAL` variables are those directly set by the user
+     and all `small-caps` variables are set by the pipeline designer. All
+     variables that also depend on this survey have a `survey` in their
+     name. Hence, also correct all these occurrences to your new name in
+     small-caps. Of course, ignore those occurrences that are irrelevant,
+     like those in this file. Note that in the raw version of this template
+     no target depends on these files, so they are ignored. Afterwards, set
+     the webpage and correct the filenames in
      `reproduce/src/make/download.mk` if necessary.
 
      ```shell