Scrivomatic docx poorly formated

Hello again, I have been trying to get scrivomatic up and running, with the help of ‘NonTroppo’

It was coming together well, but All of a sudden I am getting very poorly formatted results.

The two issues are.

(1) the paragraphs are a stream of characters, with no recognition of word breaks. so word flow over onto the next line.
(2) the footnotes are not formatted. all in have is [^fn1] etc, even though the footnotes are correctly in the .md file.

I suspect solving the first issue will solve the second.

My markdown file is as follows:

# Comment: make sure you use spaces not tabs, lower-case keys and straight quotes…
title: "PhD_Project"
  - Immanuel Koks
  - test
  - pandoc
    - paper-with-refs-docx
    - paper-no-refs-html
#    - paper-with-refs-text

# Set chapter number to match the compiled chapter (currently n=2) 
# Increment n-1 times
# One
# 1


::: {custom-style="Chapter Number"} :::

Chapter Two


::: {custom-style="Chapter Title"} :::

Common Human Experience


<!---  2 --->

# 2.1 — Breaking the Link between Brokenness and Disability  #

     In Moltmann’s discussion about including those with disabilities in the church, disability stands alongside weakness and foolishness over against strength and wisdom, etc.[^fn1] In effect, he equates disability with common notions of human lack.[^fn2] With good reason, some people object to this language or any link between disability and human brokenness.[^fn3] At first glance it infers that people with disabilities are broken while assuming those without disabilities are whole. This does nothing to recognise the common humanity we share. Presuming the opposite, that people with disabilities are whole, is also precarious. Not least, lead us to diminish the particular difficulties which many disabled people face. More to the point, however, elevating ‘whole disabled people’ over against the normal, but broken, majority is theologically unsustainable because the story of scripture is the narrative of God saving redemption of all broken, sinful humanity.[^fn4] 

     No matter how well intentioned, equating disability with brokenness and normalcy with wholeness does nothing to dispel the stigma of disability.[^fn5] To oppose the stigmatisation of people with disabilities, and in keeping with his method of de-centring normalcy, Reynolds argues that disability, not ability, is “basic” to human life.[^fn6] By doing so, Reynolds claims that disabled people are not broken, but also that disability is essential to human life. While this appears to remove the stigma of disability, it reverses the issue, but it does not get to its heart. Instead of disabled people having a problem, those without disabilities are problematised as those who mislabel those with disabilities as broken. The fundamental assumption that our brokenness makes us inferior to those who claim that they are not broken, because they don't have disabilities. 

     To be clear, I am not saying that disability is always brokenness. Rather, disabled people *experience* brokenness *like every other human being*. Nor am I categorically saying that every human diversity, which gets called an ‘impairment,’ is a broken feature of our lives, much less that those impairments are the most profound form of brokenness disabled people face. It would be naïve, however, to assume either that brokenness never causes disability, or that such a link always exists.[^fn7] Furthermore, if brokenness causes a disability, then we should not assume that the disability is the most important thing in a person’s life that God wishes to cure. Much less, that God is not at work, if he does not cure the disability. 

     Instead of shying away from acknowledging that disabled people have brokenness in their lives, I intentionally take a “people first” approach. Whatever else might be true of a disabled person, we are human beings first. Like everybody else, disabled people live with the common human experience of wholeness and brokenness. Therefore, since everyone has broken aspects of our lives, so to, those of us with disabilities. 

     Since withering and brokenness are, in fact, deeply human realities, it behold us to take the time to understand them in terms of the theological anthropology, that I have been developing. Or, more precisely, in terms of the anthropology which stems from the incarnate Christ. But, before getting there, we need to take a detour into historic christological doctrine. It is only here that find the susbstance for how we can argue that the divine Soon of God, took on our humanity.  

[^fn1]: {Moltmann, 1992 #5008@192-3}

[^fn2]: For an extended discussion about this as it applies to medicine see {Bishop, 2007 #7228@214-30}

[^fn3]: e.g. {Betcher, 2007 #8002@Loc 18-75}

[^fn4]: Notwithstanding the bookends of this story of redemption, the goodness of original creation and the heavenly hope of new creation, which are essential for understanding the fundamental goodness of creation the God is at work redeeming.

[^fn5]: {Melcher, 1998 #4919@57-59}

[^fn6]: {Reynolds, 2008 #4897@14-15, 104-5}

also here is the text from scrivomatic.log file.

=== ------------------------------------------------------ ===
=== Scrivomatic V1.0.25 Report @ 2019-07-09 12:34:52 +1200 ===
=== ------------------------------------------------------ ===
 Running under Ruby 2.3.7
 Working directory: /Users/immanuelkoks/Syncplicity Folders/PhD/Sandpit
===------ Input Options: ------===
#<struct Scrivomatic::OPT input="poor\\", output=nil, to=nil, yaml=nil, command="pandocomatic", envpath="/Users/immanuelkoks/bin:/Users/immanuelkoks/.rbenv/shims:/usr/local/bin", build=false, cleanup=false, verbose=true, dry_run=false, open_log=true, data_dir=nil>
===------ Final ENV PATH: ------===
===------ TOOL PATHS: ------===
---pandoc: /usr/local/bin/pandoc | V: 2.7.3
---pandocomatic: /Users/immanuelkoks/.rbenv/shims/pandocomatic | V: 
---ruby: /Users/immanuelkoks/.rbenv/shims/ruby | V: ruby 2.6.3p62 (2019-04-16 revision 67580) [x86_64-darwin18]
---rbenv: /usr/local/bin/rbenv
---python: /usr/bin/python

 … running pandocomatic, please wait …
===------ COMMAND OUTPUT: ------===
:: Running: /Users/immanuelkoks/.rbenv/shims/pandocomatic --debug poor\ 
::: (3) + converting /Users/immanuelkoks/Syncplicity Folders/PhD/Sandpit/poor 2 times:
::: (2)   - convert poor -> poor formatting.docx
::: pandoc	--from=markdown \
::: 	--to=docx \
::: 	--reference-doc=/Users/immanuelkoks/.local/share/pandoc/templates/chicago_thesis.docx \
::: 	--output=/Users/immanuelkoks/Syncplicity\ Folders/PhD/Sandpit/poor\ formatting.docx
::: [WARNING] Note with key 'fn1' defined at line 57 column 1 but not used.
::: [WARNING] Note with key 'fn2' defined at line 59 column 1 but not used.
::: [WARNING] Note with key 'fn3' defined at line 61 column 1 but not used.
::: [WARNING] Note with key 'fn4' defined at line 63 column 1 but not used.
::: [WARNING] Note with key 'fn5' defined at line 65 column 1 but not used.
::: [WARNING] Note with key 'fn6' defined at line 67 column 1 but not used.
::: [WARNING] Note with key 'fn7' defined at line 69 column 1 but not used.
::: (1)   - convert poor -> poor formatting.html
::: pandoc	--from=markdown \
::: 	--to=html5 \
::: 	--standalone \
::: 	--number-sections \
::: 	--section-divs \
::: 	--template=/Users/immanuelkoks/.local/share/pandoc/templates/custom.html \
::: 	--css=/Users/immanuelkoks/.local/share/pandoc/templates/custom.css \
::: 	--self-contained \
::: 	--toc \
::: 	--toc-depth=4 \
::: 	--base-header-level=1
::: pandoc: /Users/immanuelkoks/.local/share/pandoc/templates/custom.html: openBinaryFile: does not exist (No such file or directory)
::: Error running pandoc => error while running:
::: pandoc	--from=markdown \
::: 	--to=html5 \
::: 	--standalone \
::: 	--number-sections \
::: 	--section-divs \
::: 	--template=/Users/immanuelkoks/.local/share/pandoc/templates/custom.html \
::: 	--css=/Users/immanuelkoks/.local/share/pandoc/templates/custom.css \
::: 	--self-contained \
::: 	--toc \
::: 	--toc-depth=4 \
::: 	--base-header-level=1
::: Pandoc responded with:
::: pandoc: /Users/immanuelkoks/.local/share/pandoc/templates/custom.html: openBinaryFile: does not exist (No such file or directory)
:: exit status: pid 8912 exit 243

!!!---scrivomatic::runCommand() RETURN non-zero value: /Users/immanuelkoks/.rbenv/shims/pandocomatic --debug poor\ !!!

Note the warnings in the log. e.g.

::: [WARNING] Note with key ‘fn1’ defined at line 57 column 1 but not used.

Thanks again for your assistance.

Quite simple to solve, your paragraphs are all indented:

Remove the indents and compile is fine:

Now the question is where these indents are coming in — you should make sure “Show Invisibles” is turned ON in Scrivener, as indentation creates verbatim code blocks (styled in Word as “Verbatim Char”) and thus things like footnote markers will not work:

If they are not in your Scrivener source, then they may be being introduced during compile (Transformations panel in compile format editor)

p.s. you also have a missing custom.html file: “pandoc: /Users/immanuelkoks/.local/share/pandoc/templates/custom.html: openBinaryFile: does not exist (No such file or directory)” — but that only affects the html template, not the docx output…

Thanks again.

I had selected “Paragraph spacing and indents” in the “Convert to plain text” option in my scrivener format. When I just chose the “Paragraph spacing” option in worked fine.

thanks for your help