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Exemplo com FNR.exe
"C:\Users\DSCON\Desktop\fnr.exe" --cl --dir "C:\JDeveloper\mywork\POC\IGOVPAD\trunk\AppManutencaoIgovPad" --fileMask "*.jpr*" --excludeFileMask "*.dll, *.exe" --includeSubDirectories --useRegEx --find "<url n=""id"" path="".+Applications\/(.+).library""\/>" --replace "<url n=""id"" path=""../../../../../ProcessoDigital/Libraries/Comum/Applications/$1.library""/>"

Find: <url n="id" path=".+Applications\/(.+).library"\/>

Replace: <url n="id" path="../../../../../ProcessoDigital/Libraries/Comum/Applications/$1.library"/>