After some time and a few computer changes, I've decided to give Fantom a whirl. After usual problems with Hg I managed to untangle myself and try to do bootstrap the freshest version.

D:\dev\lang\fantom-1.0.55\adm>D:\dev\lang\fantom-1.0.55\bin\fan D:\dev\lang\fant
om-1.0.55\adm\bootstrap.fan -devHome file:/D:/dev/lang/fantom-hg/ -skipPull

Bootstrap Environment:
  hgRepo:    *** SKIP ***
  hgVer:     *** SKIP ***
  jdkVer:    javac 1.6.0_20 (need 1.6+)
  jdkHome:   file:/D:/dev/lang/java-1.6_20/
  relVer:    1.0.55
  relHome:   file:/D:/dev/lang/fantom-1.0.55/
  devHome:   file:/D:/dev/lang/fantom-hg/

Continue with these settings? [y|n] y
....

D:\dev\lang\fantom-hg\bin\fan.exe D:\dev\lang\fantom-hg\src\buildpods.fan compile
compile [compilerJs]
  Compile [compilerJs]
    FindSourceFiles [19 files]
    WritePod [file:/D:/dev/lang/fantom-hg/lib/fan/compilerJs.pod]
compile [concurrent]
  Compile [concurrent]
    FindSourceFiles [8 files]
    CompileJs
    WritePod [file:/D:/dev/lang/fantom-hg/lib/fan/concurrent.pod]
  javaNative [concurrent]
    Delete [file:/D:/dev/lang/fantom-hg/src/concurrent/temp-java/]
    CreateDir [file:/D:/dev/lang/fantom-hg/src/concurrent/temp-java/]
    Exec [D:\dev\lang\java-1.6_20\bin\java.exe -cp D:\dev\lang\fantom-1.0.55\lib
\java\sys.jar -Dfan.home=D:\dev\lang\fantom-hg fanx.tools.Jstub -d D:\dev\lang\f
antom-hg\src\concurrent\temp-java concurrent]
    Java Stub [concurrent]
    CompileJava
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
    Exec [D:\dev\lang\java-1.6_20\bin\jar.exe -xf D:\dev\lang\fantom-hg\src\conc
urrent\temp-java\concurrent.jar]
    Delete [file:/D:/dev/lang/fantom-hg/src/concurrent/temp-java/concurrent.jar]

    Delete [file:/D:/dev/lang/fantom-hg/src/concurrent/temp-java/meta-inf/]
    Exec [D:\dev\lang\java-1.6_20\bin\jar.exe cf D:\dev\lang\fantom-1.0.55\lib\j
ava\concurrent.jar -C D:\dev\lang\fantom-hg\src\concurrent\temp-java .]
    Exec [D:\dev\lang\java-1.6_20\bin\jar.exe -fu D:\dev\lang\fantom-1.0.55\lib\
fan\concurrent.pod -C D:\dev\lang\fantom-hg\src\concurrent\temp-java .]
java.io.IOException: Error in writing existing jar file
      at sun.tools.jar.Main.run(Main.java:217)
      at sun.tools.jar.Main.main(Main.java:1149)
ERR: Exec failed [D:\dev\lang\java-1.6_20\bin\jar.exe -fu D:\dev\lang\fantom-1.0
.55\lib\fan\concurrent.pod -C D:\dev\lang\fantom-hg\src\concurrent\temp-java .]
BUILD FAILED [5005ms]!
##
## FATAL: src/buildpods.fan compile failed
##

Any help?

It's 32 bit Java on 64-bit Win7 (because groovy doesn't want to work with 64-bit Java).

First off this is what a correct concurrent build looks like:

C:\dev\fan\src>concurrent\build
compile [concurrent]
  Compile [concurrent]
    FindSourceFiles [8 files]
    CompileJs
    WritePod [file:/C:/dev/fan/lib/fan/concurrent.pod]
  javaNative [concurrent]
    CreateDir [file:/C:/dev/fan/src/concurrent/temp-java/]
    Exec [C:\dev\tools\java\bin\java.exe -cp C:\dev\fan\lib\java\sys.jar -Dfan.home=C:\dev\fan fanx.tools.Jstub -d C:\de
v\fan\src\concurrent\temp-java concurrent]
    Java Stub [concurrent]
    CompileJava
Note: Some input files use unchecked or unsafe operations.
  Note: Recompile with -Xlint:unchecked for details.
  Exec [C:\dev\tools\java\bin\jar.exe -xf C:\dev\fan\src\concurrent\temp-java\concurrent.jar]
    Delete [file:/C:/dev/fan/src/concurrent/temp-java/concurrent.jar]
    Delete [file:/C:/dev/fan/src/concurrent/temp-java/meta-inf/]
    Exec [C:\dev\tools\java\bin\jar.exe cf C:\dev\fan\lib\java\concurrent.jar -C C:\dev\fan\src\concurrent\temp-java .]
    Exec [C:\dev\tools\java\bin\jar.exe -fu C:\dev\fan\lib\fan\concurrent.pod -C C:\dev\fan\src\concurrent\temp-java .]
    Delete [file:/C:/dev/fan/src/concurrent/temp-java/]
BUILD SUCCESS [22443ms]!

Note that concurrent is not bootstrap, therefore it should be using nothing from your release dir (in your case 1.0.55 dir). But it appears that in your case that it is are using the wrong directory. If you have bootstrap built to the point where you have sys.jar and sys.pod, compiler.pod in your fantom-hg/lib directory, then just put fantom-hg/bin into your path and try rebuilding concurrent that way.

Nvm, figured I missed a part of the documentation about substitutes.