How do I upgrade my existing LyX system to version 1.0.4?
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If you upgrade from version 0.12.0 or 1.0.x, you shouldn't have 
any problems.  Just run "make install", and it will automatically
update the necessary files, provided that you install LyX the
same place as an existing version.

Document transfer
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In general, you don't need to convert any documents saved with LyX
v0.10, v0.12.0 or v1.0.x to use them with LyX v1.0.4.

LyX v1.0.x can read all documents saved with lyx-0.12.0 and later correctly.
Documents saved with lyx-0.10.x are read correctly up to the old math 
mode, which is not supported anymore. If you have documents with such 
math formulas, you convert it using the program COLD, written by Preben 
Rhandol. COLD can be found at:

  http://www.pvv.org/~randhol/lyx/COLD/
  ftp://ftp.lyx.org/pub/lyx/contrib/

or at one of LyX archive mirror sites listed in README.

Documents saved with LyX version 1.0.4 can be read correctly by 
LyX v0.12.0 and v1.0.x, except for new features.