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From: Ralf Angeli <dev.null@caeruleus.net>
Newsgroups: gmane.emacs.help
Subject: Re: Then how to replace all my $$ ... $$ to \[ \] through search
	and replace?
Date: Fri, 15 Aug 2008 12:13:38 +0200
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* Phil Carmody (2008-08-15) writes:

> Tassilo Horn <tassilo@member.fsf.org> writes:
>> Ralf Angeli <dev.null@caeruleus.net> writes:
>>
>>>> M-x query-replace-regexp RET \$\$\(.+\)\$\$ RET \\[\1\\] RET
>>>
>>> This won't work because `.' does not match a newline.
>>
>> Ok, but at least it works for oneliners.
>>
>>> Using `[^$]' instead should do it.
>>
>> Right, that's better.
>
> $$ What about this $1,000,000 example? $$

Then you could use something like

C-M-% \$\$ <RET> \,(if (zerop (mod \# 2)) "\\[" "\\]") <RET>

-- 
Ralf