If you are using TeX Live, you don't need to run texhash when adding files to your personal tree. However, I wouldn't add your customised texmf.cnf there. Probably TeXworks starts a new shell for a compilation run which likely doesn't read ~/.bashrc.
Better would be to create the file somewhere your TeX installation will look by default anyway. On TeX Live, for example, read the notes at the top of texmf-dist/web2c/texmf.cnf. On a Unix-type system (e.g. Mac OS X, GNU/Linux, BSD etc.) you can get the full path to the file using $(kpsewhich -var TEXMFMAIN)/web2c/texmf.cnf. On my system, for example
echo $(kpsewhich -var TEXMFMAIN)/web2c/texmf.cnf
returns
/usr/local/texlive/2015/texmf-dist/web2c/texmf.cnf
This file includes instructions for how and where to include modified settings. For example, mine says this:
% original texmf.cnf -- runtime path configuration file for kpathsea.
% Public domain.
%
% If you modify this original file, YOUR CHANGES WILL BE LOST when it is
% updated. Instead, put your changes -- and only your changes, not an
% entire copy! -- in ../../texmf.cnf. That is, if this file is
% installed in /some/path/to/texlive/2015/texmf-dist/web2c/texmf.cnf,
% add your custom settings to /some/path/to/texlive/2015/texmf.cnf.
%
% What follows is a super-summary of what this .cnf file can
% contain. Please read the Kpathsea manual for more information.
%
% Any identifier (sticking to A-Za-z_ for names is safest) can be assigned.
% The `=' (and surrounding spaces) is optional.
% $foo (or ${foo}) in a value expands to the envvar or cnf value of foo.
% Long lines can be continued with a \.
%
% Earlier entries (in the same or another file) override later ones, and
% an environment variable foo overrides any texmf.cnf definition of foo.
%
% All definitions are read before anything is expanded, so you can use
% variables before they are defined.
%
% If a variable assignment is qualified with `.PROGRAM', it is ignored
% unless the current executable (last filename component of argv[0]) is
% named PROGRAM. This foo.PROGRAM construct is not recognized on the
% right-hand side. For environment variables, use FOO_PROGRAM.
%
% Which file formats use which paths for searches is described in the
% various programs' and the Kpathsea documentation (http://tug.org/kpathsea).
%
% // means to search subdirectories (recursively).
% A leading !! means to look only in the ls-R db, never on the disk.
% In this file, either ; or : can be used to separate path components.
% A leading/trailing/doubled path separator in the paths will be
% expanded into the compile-time default. Probably not what you want.
%
% Brace notation is supported, for example: /usr/local/{mytex,othertex}
% expands to /usr/local/mytex:/usr/local/othertex. We make extensive
% use of this.
Following these instructions, my modifications are in $(kpsewhich -var TEXMFMAIN)/../texmf.cnf which includes the following header:
% (Public domain.)
% This texmf.cnf file should contain only your personal changes from the
% original texmf.cnf (for example, as chosen in the installer).
%
% That is, if you need to make changes to texmf.cnf, put your custom
% settings in this file, which is .../texlive/YYYY/texmf.cnf, rather than
% the distributed file (which is .../texlive/YYYY/texmf-dist/web2c/texmf.cnf).
% And include *only* your changed values, not a copy of the whole thing!
%
followed by settings for just the bits I want to modify:
%%
% ref.: norbert's answer at http://tex.stackexchange.com/a/262265/
TEXMFARCH = /usr/share/texmf
TEXMF = {$TEXMFCONFIG,$TEXMFVAR,$TEXMFHOME,!!$TEXMFSYSCONFIG,!!$TEXMFSYSVAR,!!$TEXMFLOCAL,!!$TEXMFDIST,$TEXMFARCH}
TEXMFDBS = {!!$TEXMFSYSCONFIG,!!$TEXMFSYSVAR,!!$TEXMFLOCAL,!!$TEXMFDIST,$TEXMFARCH}
This should work fine whether you compile from the command line or from within an editor such as TeXworks.
texhashwhen adding files to your personal tree. Probably TeXworks starts a new shell for a compilation run which likely doesn't read~/.bashrc. Better would be to create the file somewhere your TeX installation will look by default anyway. On TeX Live, read the notes at the top oftexmf-dist/web2c/texmf.cnf. – cfr Aug 25 '15 at 13:27texmf.cnfbecause you are compiling large TikZ pictures. What changes are you making exactly? – cfr Aug 25 '15 at 13:28texmf.cnfin the root directory of my TeX Live installation (on OSX:/usr/local/texlive/2015/withrootrights) as written intexmf-dist/web2c/texmf.cnf. Now it's working!! – Guuk Aug 25 '15 at 13:38pgfplotsmanual section 6.1. – Guuk Aug 25 '15 at 13:39