Yes, I agree. The remaining problem need many simultaneos rare conditions to show, and even in that case, it is ignorable as the cause is known to not harm...

In a clean git clone, a ./make went without errors this time. The timestamps could have been in order by chance. Then touching all .jpg in test/ and doing again a ./make it went correct. And at last touching all .png in test/ and repeating ./make all was ok.

I am not sure also about what is best, but probably the solution should be different for each test case:
If the objective of a test is to detect conversion from one format to other, then the target must be removed before running that test. In this case it should be natural to have error messages when convert (imagemagick) is not correctly or fully installed (as in my case). Also that graphic file can (must?) be removed from git.
On the other hand, if the objective of the test is to find differences in the html files that depend on a correct graphic file, then it is necessary to check if the target graphic file already exists and, only in this case, touch it to ensure no conversion is done before running elyxer in the test.
The graphic test files must be separated in different sets, one for persistent graphics and other for erasable ones, and the later set could be removed from git also.

Tried again in clean git clone and now almost all goes OK, except an strange problem in doc generation phase (remember I have imagemagick but without rsvg).
eLyXer tried to convert "docs/parse tree.svg" (so giving an error by convert), but the file "docs/parse tree.png" was already in git. The other .svg/.png files in docs were OK, so at first I thought it was a problem with space in name or similar.
Finally, the problem is that timedate stamp of .png file was earlier than the corresponding .svg, so eLyXer tried to rebuild the .png.
This different timestamp is the result of undefined order of download by git. And  it could explain why you cannot reproduce the other problem reported in my previous comment #5 with test/laurindas-anger.png, this could occur in random files with each new clean git clone...
The solution is to just "touch" all the .png and .jpg files in docs before using them in ./make, to ensure they are newer than their .svg.

On the other hand, I tried a new git clone and a blind touch of all jpg and png in subdirectories (including tests), but then I got a difference in test "with images-1-5-jpg-test.html" about dimensions in "square.jpg" because it is not converted from .svg but from .png, that my installation of imagemagick is able to do, but for some reason it results in different size:

Testing eLyXer -- any text below this line signals an error
--- with images-1-5-jpg-good.html        2010-10-26 01:37:21.481196835 +0200
+++ with images-1-5-jpg-test.html        2010-10-26 01:53:21.968696912 +0200
@@ -30,7 +30,7 @@
 Fourth image: from a JPEG file.
 </div>
 <div class="Standard">
-<img class="embedded" src="square.jpg" alt="figure square.jpg" style="width: 300px; max-width: 30px; height: 300px; max-height: 30px;"/>
+<img class="embedded" src="square.jpg" alt="figure square.jpg" style="width: 30px; max-width: 3px; height: 30px; max-height: 3px;"/>
 Fifth image: from a PNG file.
 </div>

This could be a sign that if all the converted images in tests are already included from git, then they are not really checked by conversion, but just from the downloaded version if timestamp is newer...

The rest of issues (language, etc.) are OK.

Testing ./make in a clean new git clone (with imagemagick installed but without rsvg):

1. Now there is no error about images during docs building phase (just progress messages and one "Line 3082: . Unknown command \Game").

2. During tests there are only 2 failures in image conversion but they seem related to not finding the files `test/laurindas-anger.png' and `laurindas-anger.png'. I can see there is only a "laurindas-anger.png" but in "test/subdir/".

On the other hand, there is no detected failure for converting any svg file in tests, because all the corresponding .jpg and .png are already included in git. Check the "test" subdir in git tree http://git.savannah.gnu.org/cgit/elyxer.git/tree/test

And there is also a small difference. In test "descriptions-1-5-good.html" appears the old Spanish translation "Glosario" and, as I have installed the new file elyxer.mo, in "descriptions-1-5-test.html" appears the new "Índice alfabético". This is minor, but it hints that the tests should be run with "export LANG=C" environment and that "good" files should be generated also with LANG=C, so to avoid false differences due to different locales.
 
3. (to be checked in next release).
4. OK.
5. OK.

Yes, now bootstrap of conf/config.py works from git version and, independent of other messages (see comment #1), an elyxer.py file is created correctly.

After copying config.py from 1.0.3, to avoid the bootstrap problem in the git version (in original post in this bug), running ./make builds elyxer.py, but it prints some errors during documentation building, all of them similar to the following:

sh: rsvg: not found
convert: delegate failed `"rsvg" "%i" "%o"' @ error/delegate.c/InvokeDelegate/1061.
convert: unable to open image `/tmp/magick-XXm6PhM8': gick-6.6.0/modules-Q16/coders/svg.la @ error/blob.c/OpenBlob/2489.
convert: unable to open file `/tmp/magick-XXm6PhM8': ���� @ error/constitute.c/ReadImage/572.
convert: missing an image filename `docs/elyxer.png' @ error/convert.c/ConvertImageCommand/2940.
Line 72: * imagemagick not installed; images will not be processed

imagemagick is installed, but as I use inkscape to convert .svg files in LyX,
"rsvg" program (used by imagemagick) is not needed, so I already do not have installed Debian package librsvg2-bin that has it.

I just copied files: container.png, elyxer.png, parse\ tree.png, pipeline.png, from docs directory in elyxer-1.0.3.tar.gz and then ./make in git version worked.
Maybe, those files for documentation must be included in git to avoid strange failure messages before the tests.

On the other hand, maybe, run-tests (if it is not tested previously in ./make) should include a test to see if "convert" (from imagemagick) is installed, and if it is being able to convert from svg to png (i.e.: rsvg is installed) and in case it fails, then it could try with inkscape (to set it by default or warning, in case it can), or if it both converters fail, then show a clear message urging to install rsvg or to check imagemagick installation, etc.

---

I have seen that .tar.gz distribution (not in git) includes all the "...-test..." files, so run-tests could not detect if a test failed to create the file, because it already is there from start...

---

Also I only have Python 2.6 (default in Debian now) and don't have Python 2.4 installed, so cannot test  index-1-6-py2.4-test.html in ./run-tests, but it generates an error. Probably, the following in run-tests could be better:

type -P python2.4 &> /dev/null
if [ $? = 0 ] ; then
   name="index-1-6"
   python2.4 ../elyxer.py --quiet --css ../docs/lyx.css "$name.lyx" "$name-py2.4-test.html"
   diff -u --ignore-matching-lines="create-date" "$name-good.html" "$name-py2.4-test.html"
else
   # echo "python2.4 not found, cannot test it"
fi

Thanks.