I am testing BaKoMa, opened one simple document (a thesis template) and get an error when BaKoMa tries to open ifetex.sty, although I can see the file is where expected This is e-TeX, Version 3.14159265-2.6 (BaKoMa TNS 9.0) entering extended mode (Plantilla-TFM.tex LaTeX2e <2016/03/31> patch level 3 Babel <3.9r> and hyphenation patterns for 55 language(s) loaded. (C:\Users\dtroigl\OneDrive\Tex\texmf\tex\latex\nag\nag.sty (C:\Users\dtroigl\OneDrive\Tex\texmf\tex\latex\nag\nag-l2tabu.cfg)) (C:\Users\dtroigl\OneDrive\Tex\texmf\tex\latex\memoir\memoir.cls Document Class: memoir 2016/05/16 v3.7f configurable book, report, article docu ment class (C:\Users\dtroigl\OneDrive\Tex\texmf\tex\generic\oberdiek\ifpdf.sty) (C:\Users\dtroigl\OneDrive\Tex\texmf\tex\latex\ifetex\ifetex.sty ! I can't find file `ifetex'. l.22 \@@input ifetex Please type another input file name: ! Emergency stop. l.22 \@@input ifetex

The package ifetex is:
$TEXMF/tex/latex/ifetex/ifetex.sty

It requires the file ietex.tex, which is in folder:
$TEXMF/tex/plain/ifetex/ifetex.tex

However, BaKoMa TeX reads folders 'latex' and 'generic' as recommended by TeX Directory Standard:
ftp://ftp.dante.de/tex-archive/tds/tds.html#Macros

TeXLive, finally, searches also top of folder ($TEXDIR/tex//),
it is probably to avoid such situations with wrongly placed package components.

How to solve the problem ?

Simplest way si to add search in plain folder in TEXMF.INI file.

So, for e-LaTeX I suggest following change:

[ELATEX]
ID=e-LaTeX 2e
Check=elatexelatex.ini&elatexlatex.ltx
Format=eLaTeX.ini
FormatName=eLaTeX
;TEXINPUTS=.;$TEXMF/tex/{etex,latex,generic,latex209}${$}
TEXINPUTS=.;$TEXMF/tex/{etex,latex,generic,latex209,plain}${$}
TeXProcessor=eTeX
TeXFormatExtension=efmt
Syntax=LATEX
Info=LaTeX 2e with Extended TeX (e-TeX) processor.

Note,
old string:
TEXINPUTS=.;$TEXMF/tex/{etex,latex,generic,latex209}${$}
new string:
TEXINPUTS=.;$TEXMF/tex/{etex,latex,generic,latex209,plain}${$}

Version 11.21 (for Windows) revision 170127 includes this fix.

Just download it and agree to update.
All records in TEXMF.INI will be fixed.