Markdown don't allow space in the filenames. So encode to %20 to replace the space in the filenames.
e.g.
([ontology](2.1 Ontologies.md))
should be
([ontology](2.1%20Ontologies.md))
For example, you have a repo like the following:
project/
text.md
subpro/
subtext.md
subsubpro/
subsubtext.md
subsubpro2/
subsubtext2.md
subtext.md in text.md might look like this:[this subtext](subpro/subtext.md)
subsubtext.md in text.md might look like this:[this subsubtext](subpro/subsubpro/subsubtext.md)
subtext.md in subsubtext.md might look like this:[this subtext](../subtext.md)
subsubtext2.md in subsubtext.md might look like this:[this subsubtext2](../subsubpro2/subsubtext2.md)
[this text](../../text.md)
| a | r |
|------------|-----|
| `a += x;` | r1 |
|a |= y; | r2|
| a | r |
|---|---|
a += x; | r1 |
| a |= y; | r2 |
and
| a | r |
|------------|-----|
| `a += x;` | r1 |
|<code>a |= y;</code> | r2|
| a | r |
|---|---|
a += x; | r1 |
a |= y; | r2 |