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It seems that the orphans plugin doesn't recognize markdown-style links of the kind:
[Pretty link name](realname)
In my wiki, the page "realname" shows up as an orphan although it's being linked to.
Like anything in ikiwiki that deals with links, this only takes
[[WikiLinks|ikiwiki/wikilink]] into account. There should be no real
reason to use other link mechanisms provided by eg, markdown for internal
links in the wiki (indeed, using them is likely to cause broken links
when doing things like inlining or renaming pages). --[[Joey]]
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