I thought I had a way to make Bibliography appear in the TOC, but I cannot reproduce it now. It apparently doesn't have to do with the Document Class options: bibtotoc (but Nomenclature appears in test/index-1.6.lyx, maybe idxtotoc). I don't know what to do without more information about LyX (or LaTeX) options.

Your problem with BibTeX bibliography and separate entries is probably due to a repeated #Bibliography anchor. I should just remove the Bibliography anchor for the separate bibliography entries and leave it as is until I get more information, but I kind of like having all level-1 items in the TOC. What do you think?

There was another bug here: bibliography items (inserted as separate layouts) did generate a big Bibliography header, but it was not being added to the TOC. I have corrected it now.

I think that remaining issues in point 2 of this bug need to be clarified:

When the Bibliography list (bibtex) is inside a comment, then the expected behaviour for eLyXer should be to not show it in TOC (independently of the show -in-toc option state in LyX inset) and to not show the corresponding chapter/section with the list of references at the end of document (independently of the show-all-refs option in LyX inset).
The second part is already working this way in eLyXer (git version), but not the first part (bibliography already appears in TOC even when it is inside a comment).

The behaviour of normal citations (not inside comment) when the bibliography is inside a comment is undefined and any behaviour is acceptable for eLyXer in this case (LaTeX shows "[??]" and eLyXer a label-link to nowhere), because it is the fault of the document author to supply the bibiliography correctly.

I have not thought about the citation itself inside a comment until now, reading your last comment #7, and as I can see eLyXer now does not show the citation, but it shows the reference in the bibliography list as if the citation was used. I agree that this behavior (different with LaTeX)  is a minor problem that can go as a suggestion to the wish-list because it could be usefull only in some cases.

In any case, of course you don't need my permission to treat the bug reports in the order or with the priority you feel are better. You are already doing an impressive work with eLyXer and most of these bugs are just strange and corner cases.
Best regards,
Jose R.

I cannot find an exhaustive list of all "documentclass" supported by LyX layouts, but I have found that there are at least the following book/report type "documentclass":  
      [ book, amsbook, scrbook, extbook, tufte-book, report, extreport, scrreprt, memoir, tbook, jsbook, jbook, mwbk, svmono, svmult, treport, jreport, mwrep ]
Their first autonumbered level is 0 (\chapter), and they can have independent numbered level -1 (\part), with\bibname = "Bibliography".
     
On the other hand article/paper type of "documentclass" like article, paper, extarticle, seminar, amsart, and a lot of other journal specific papers, have first numbered level is 1 (\section), but they can have also independent numbered level -1 (\part) with \bibname = "References".

Note: In closed bug #31342  http://savannah.nongnu.org/bugs/index.php?31342 , I forgot to mention that Part numbers in LaTeX and LyX are uppercase roman...

Additionally, I found that there is a third kind of "documentclass":
      [letter, extletter, dinbrief, g-brief, g-brief2, scrlttr2, scrlettr, slides, beamer, foils, powerdot, tufte-handout, simplecv, europecv, moderncv, broadway, hollywood ]
that don't have autonumbered hierarchical sectioning levels or have only special labels for few numbered sections (act, scene). Fortunatelly, this kind of documents should not have numbered sections, and most of them cannot handle a Bibliography, so, probably, it is not neccesary to take any special care with them in eLyXer.

Until now, I was just navigating in git tree and logs through web interface, but I can (and will do from now on) import git tree and use "./make" to build elyxer.py for tests, so you will not need to upload elyxer.py each time.
I found a problem in this process that I have reported in a different bug.

Thanks.

Hi, I can see a lot of work and changes in this version.

1. Yes, corrected.

2. OK support for LyX option to show bibliography in TOC if requested. But the bibliography already appears in TOC when it is inside a comment (and option to show selected).
   Sorry, but probably my initial report was not well explained in this point (English is not my mother language) or I don't understand your comment: "[...]that the bibliography is being added to the document even if inside a comment, yet."
   The expected behavior for eLyXer (mimicking LyX/LaTeX) if a Bibliography is inside a comment, should be to not show it in text and to not show it in TOC. Of course, when bibliography is inside a comment, the citations in text cannot link to any point and they are shown as "[??]" in LaTeX/PDF, and something similar could be done in eLyXer in this case. If bibliography is inside a comment, it is the responsability for the document author to provide the correct bibliography for citations or to not cite them.

3. All styles correct with commited .css.
   But with "--splitpart 1" the Bibliography is always at the end of the previous chapter/section (no different page), while the Nomenclature and Index correctly get a separated page like the level 1 (chapter in book of Section in article). In LaTeX/LyX, for book and report types, Bibliography starts in a new page like Nomenclature and Index, while in other documents all of them continue in the same page. It should be natural for eLyXer to separate in a new page all elements in the same level (Bibliography, Nomenclature and Index) when requested by splitpart option.

4. Yes (seen committed in .po file).

Also, I can see the string "Bibliography" has changed to "References" (and corresponding translations) for all document types (or so it seems), but I have some points about it:
The command "\bibname" in LaTeX contains the string "Bibliography" (and translations) for book and report type documents, and the string "References" (and translations) for the rest of types. LyX uses "Bibliography" in GUI and menus, but it show the correct label "References" or "Bibliography" inside the text preview depending on document type.
There is a subtle difference in the meaning of both terms:
   "Bibliography" can be the list of works used by author to produce the document (even if they are not referenced explicitly in the text). This term is used in books as it is usual to include in the list also other works not cited but used in general (as with option to show all bibentries now supportted in eLyXer).
   "References" is the list of works referenced or cited by author in the text of document. This name is more common in short documents (articles, papers, etc.) to reflect the nature of the list of works as citations.
   
Thanks!

More comments:

1. The first issue is more generic than described: all TOC entries are shown in the TOC (chapters, sections...), even if they are inside comments. They are also considered for numbering: if Chapter 2 is inside a comment, the next chapter will be Chapter 3 for eLyXer (but another Chapter 2 for LyX and on the PDF output).

1. Index and Nomenclature inside a comment note are shown in text and in Table of contents, they should be not shown in this case.
It could be useful to have Index or Nomenclature inside a comment while developing early versions of a document with very incomplete Index, etc.

2. Bibliography is never shown in Table of contents, but Bibliography inside a comment is always shown in text. In LyX there is an option to show Bibliography in TOC. It would be nice if eLyXer could support it (except if Bibliography is inside a comment).
A Bibliography inside a comment could have sense if you want to be able to see cites from the bib file through LyX GUI while working on document, but you don't want the bibliography to be shown yet in current document, or when none reference is cited yet, etc.

3. Bibliography, Index and Nomenclature should have the same style as the first level (section in article or chapter in book) unnumbered, both in text and in table of contents. In eLyXer now they are shown as level 2 or smaller.

4. In eLyXer Spanish locale "Index" is incorrectly translated into "Glosario", but in LyX and in LaTeX it is translated as "Índice alfabético".
Probably in LaTeX (and LyX), the "Nomenclature" should have been named "Glossary", that describes more accurately its real funcion (list of terms with description or definition), but it cannot be applied to "Index" (a list without description).

Best regards,
Jose R.