I'm running rather long documents through Spacy, and would like to retain position markers of paragraphs in the Spacy doc but ignore them in the parse. I'm doing this to avoid creating a lot of different docs for all the paragraphs.
Example using XPath:
\\paragraph[@id="ABC"] This is a test sentence in paragraph ABC
I'm looking for a bit of direction here. Do I need to add entities/types or implement a customized tokenizer? Can I use the matcher with a callback function to affect that specific token?
Your Environment

Installed models: en
Python version: 3.4.2
spaCy version: 1.8.1
Platform: Linux-3.16.0-4-686-pae-i686-with-debian-8.6
spaCy's tokenizer is non-destructive, so you can always find your way back to the original string -- text[token.idx : token.idx + len(token)] will always get you the text of the token.
So, you should never need to embed non-linguistic metadata within the text, and then tell the statistical model to ignore it.
Instead, make the metadata a standoff annotation, that holds a character start and end point. You can always make a labelled Span object after the doc is parsed for your paragraphs.
Btw, in order to keep the alignment, spaCy does have tokens for significant whitespace. This sometimes catches people out.
Spacy: Retain position markers in string, ignore them in Spacy