Display and format of section and subsection in RTL (Hebrew)

Question

I have come across a very peculiar problem. The sections and subsections show correctly in my output when the language is set to English. But when I change the language to Hebrew which it needs to be to display the RTL language correctly, the sections and subsections are messed up. I need to understand why this is happening and how to fix it, please.

The only change between the two examples is \setmainlanguage{english} changed to \setmainlanguage{hebrew}.

An ideal answer would use the hebrewnumerals feature, but show only the relevant subsection and section parts of the number. As in 2 instead of 1.1.2 or rather ב instead of א.א.ב

Example 1:

Example 2:

MWE: (compile it in XeLaTeX with Cardo font)

\documentclass[paper=a5,pagesize=pdftex]{scrbook}
\usepackage[top=2cm,bottom=1.5cm, left=1.5cm, right=1.5cm]{geometry}
\usepackage[pagestyles]{titlesec}
\usepackage{lettrine}
\usepackage{xltxtra}
\usepackage{tocloft}
\usepackage{etoolbox}
\usepackage[toc]{multitoc}
\usepackage{setspace}

\renewcommand{\thesection}{\arabic{section}}
\renewcommand{\thesubsection}{\arabic{subsection}}

\setcounter{tocdepth}{0}
\setcounter{secnumdepth}{2}

\defaultfontfeatures{Mapping=tex-text}
\setmainfont{Cardo}

% sets the marks to be used (section and subsection)
\setmarks{section}{subsection}

\newlength\howwide

\newcommand\defhowwide{
    \ifnumless{\value{section}}{99}{\ifnumgreater{\value{section}}{8}{\setlength{\howwide}{2.5em}}{\setlength{\howwide}{1.2em}}}{\ifnumgreater{\value{section}}{98}{\setlength{\howwide}{3.5em}}{\setlength{\howwide}{2.5em}}}
}

% sections and subsections formatting
\titleformat{\section}{}{\lettrine{\thesection}}{0em}{}[\vskip-1\baselineskip]
\titleformat{\subsection}[runin]{\small\bfseries}{\thesubsection}{1em}{}
\titlespacing{\section}{\howwide}{-1pt}{0pt}
\titlespacing{\subsection}{0pt}{0pt}{1em}

\setlength{\parindent}{0pt}

\newlength\NumLen
\newlength\LinLen
% indents one line of text. Indentation= width of section number + 1em
\newcommand\IndOne{%
  \setlength\NumLen{\howwide}
  \addtolength\NumLen{0.5em}
  \setlength\LinLen{\dimexpr\textwidth-\NumLen}%\the\NumLen\the\LinLen
  \parshape 2 \NumLen \LinLen 0pt \textwidth}
% indents two lines of text. Indentation= width of section number + 1em
\newcommand\IndTwo{%
  \setlength\NumLen{\howwide}
  \addtolength\NumLen{0.5em}
  \setlength\LinLen{\dimexpr\textwidth-\NumLen}%\the\NumLen\the\LinLen
  \parshape 3 \NumLen \LinLen \NumLen \LinLen 0pt \textwidth}

\usepackage{polyglossia} 
   \setmainlanguage{english} 
   \setotherlanguage{english}

\begin{document}

\mainmatter

\newlength{\myIndent}
\setcounter{section}{0}

\addtocounter{chapter}{1}

\setcounter{section}{0}
\defhowwide
\section{}
\settowidth{\myIndent}
{\IndOne בְּרֵאשִׁית בָּרָא אֱלֹהִים אֵת הַשָּׁמַיִם וְאֵת הָאָרֶץ׃}
\ifdimless{\the\myIndent}
{\textwidth-\howwide+0.75em}
{\IndOne בְּרֵאשִׁית בָּרָא אֱלֹהִים אֵת הַשָּׁמַיִם וְאֵת הָאָרֶץ׃ \stepcounter{subsection}
\subsection{} \IndOne וְהָאָרֶץ הָיְתָה תֹהוּ וָבֹהוּ וְחֹשֶׁךְ עַל־פְּנֵי תְהֹום וְרוּחַ אֱלֹהִים מְרַחֶפֶת עַל־פְּנֵי הַמָּיִם׃}
{\IndTwo בְּרֵאשִׁית בָּרָא אֱלֹהִים אֵת הַשָּׁמַיִם וְאֵת הָאָרֶץ׃ \stepcounter{subsection} \subsection{} וְהָאָרֶץ הָיְתָה תֹהוּ וָבֹהוּ וְחֹשֶׁךְ עַל־פְּנֵי תְהֹום וְרוּחַ אֱלֹהִים מְרַחֶפֶת עַל־פְּנֵי הַמָּיִם׃}
\subsection{} וַיֹּאמֶר אֱלֹהִים יְהִי אֹור וַיְהִי־אֹור׃
\end{document}

Answer 1

The main problem is probably that you are defining commands before you load polyglossia. Since polyglossia loads the bidi package when you select an RTL language, and bidi does all sorts of modifications to package commands, it's important to do all of your own modifications after loading polyglossia and setting the language.

In general, this is good practice independent of polyglossia: first load packages, then do command (re)definitions.