FULL PRODUCT VERSION :
C:\Program Files\Java\jdk1.8.0_161\bin>java -version
java version "1.8.0_161"
Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 6.3.9600]

A DESCRIPTION OF THE PROBLEM :
This is on a server running Jenkins CI using 1.8.0_161 x64 JRE.

For some debug information on a hanging java thread I needed jcmd, so downloaded the sibling JDK, got my thread dumps and then continued, only to discover that Jenkins is now unable to start any java process:

[tools] $ cmd.exe /C "c:\jenkins\tools\hudson.tasks.Ant_AntInstallation\Ant\bin\ant.bat -file build.xml -Ddlc=oe11.6 update-json-demo-database && exit %%ERRORLEVEL%%"
'"java.exe"' is not recognized as an internal or external command,
operable program or batch file.
Build step 'Invoke Ant' marked build as failure

Looking at the folders - I found out that my JRE installation had been wiped out - for as far as the JDK installer could. Some files were really really in use and could not be wiped.

The in use files frustate the issue even further since the in use files prevent any repair attempt since the JRE installer refuses to install in a directory that is not empty.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. install JRE
2. install JDK
3. look at JRE folder
4. gasp - the JRE folder has been wiped out


EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
4. smile - the JRE folder is still in place

ACTUAL -
4. gasp - the JRE folder has been wiped out

REPRODUCIBILITY :
This bug can be reproduced always.