ADDITIONAL SYSTEM INFORMATION :
Linux
Property settings:
    file.encoding = UTF-8
    file.separator = /
    java.class.path =
    java.class.version = 69.0
    java.home = /usr/lib/jvm/java-25-openjdk-amd64
    java.io.tmpdir = /tmp
    java.library.path = /usr/java/packages/lib
        /usr/lib/x86_64-linux-gnu/jni
        /lib/x86_64-linux-gnu
        /usr/lib/x86_64-linux-gnu
        /usr/lib/jni
        /lib
        /usr/lib
    java.runtime.name = OpenJDK Runtime Environment
    java.runtime.version = 25.0.2+10-Ubuntu-124.04
    java.specification.name = Java Platform API Specification
    java.specification.vendor = Oracle Corporation
    java.specification.version = 25
    java.vendor = Ubuntu
    java.vendor.url = https://ubuntu.com/
    java.vendor.url.bug = https://bugs.launchpad.net/ubuntu/+source/openjdk-25
    java.version = 25.0.2
    java.version.date = 2026-01-20
    java.vm.compressedOopsMode = Zero based
    java.vm.info = mixed mode, sharing
    java.vm.name = OpenJDK 64-Bit Server VM
    java.vm.specification.name = Java Virtual Machine Specification
    java.vm.specification.vendor = Oracle Corporation
    java.vm.specification.version = 25
    java.vm.vendor = Ubuntu
    java.vm.version = 25.0.2+10-Ubuntu-124.04
    jdk.debug = release
    line.separator = \n
    native.encoding = UTF-8
    os.arch = amd64
    os.name = Linux
    os.version = 6.17.0-14-generic
    path.separator = :
    stderr.encoding = UTF-8
    stdin.encoding = UTF-8
    stdout.encoding = UTF-8
    sun.arch.data.model = 64
    sun.boot.library.path = /usr/lib/jvm/java-25-openjdk-amd64/lib
    sun.cpu.endian = little
    sun.io.unicode.encoding = UnicodeLittle
    sun.java.launcher = SUN_STANDARD
    sun.jnu.encoding = UTF-8
    sun.management.compiler = HotSpot 64-Bit Tiered Compilers
    user.country = DE
    user.dir = /tmp/canonical-path-test
   

openjdk version "25.0.2" 2026-01-20
OpenJDK Runtime Environment (build 25.0.2+10-Ubuntu-124.04)
OpenJDK 64-Bit Server VM (build 25.0.2+10-Ubuntu-124.04, mixed mode, sharing)

Windows
Property settings:
    file.encoding = UTF-8
    file.separator = \
    java.class.path =
    java.class.version = 69.0
    java.home = c:\Program Files\Eclipse Adoptium\jdk-25.0.2.10-hotspot
    java.io.tmpdir = C:\Users\bodewig\AppData\Local\Temp\
    java.library.path = c:\Program Files\Eclipse Adoptium\jdk-25.0.2.10-hotspot\bin
        C:\WINDOWS\Sun\Java\bin
        C:\WINDOWS\system32
        C:\WINDOWS
        C:\Program Files\Eclipse Adoptium\jdk-21.0.10.7-hotspot\bin
        C:\Program Files\Eclipse Adoptium\jdk-25.0.2.10-hotspot\bin
        C:\WINDOWS\system32
        C:\WINDOWS
        C:\WINDOWS\System32\Wbem
        C:\WINDOWS\System32\WindowsPowerShell\v1.0\
        C:\Program Files\dotnet\
        C:\WINDOWS\System32\OpenSSH\
        C:\Program Files\PowerShell\7\
        C:\Program Files\Git\cmd
        C:\Users\bodewig\.dotnet\tools
        C:\Windows\Microsoft.NET\Framework\v4.0.30319
        C:\Users\bodewig\AppData\Local\Microsoft\WindowsApps
        C:\Users\bodewig\.dotnet\tools
        C:\xmlunit
        .
    java.runtime.name = OpenJDK Runtime Environment
    java.runtime.version = 25.0.2+10-LTS
    java.specification.name = Java Platform API Specification
    java.specification.vendor = Oracle Corporation
    java.specification.version = 25
    java.vendor = Eclipse Adoptium
    java.vendor.url = https://adoptium.net/
    java.vendor.url.bug = https://github.com/adoptium/adoptium-support/issues
    java.vendor.version = Temurin-25.0.2+10
    java.version = 25.0.2
    java.version.date = 2026-01-20
    java.vm.compressedOopsMode = Zero based
    java.vm.info = mixed mode, sharing
    java.vm.name = OpenJDK 64-Bit Server VM
    java.vm.specification.name = Java Virtual Machine Specification
    java.vm.specification.vendor = Oracle Corporation
    java.vm.specification.version = 25
    java.vm.vendor = Eclipse Adoptium
    java.vm.version = 25.0.2+10-LTS
    jdk.debug = release
    line.separator = \r \n
    native.encoding = Cp1252
    os.arch = amd64
    os.name = Windows 11
    os.version = 10.0
    path.separator = ;
    stderr.encoding = cp437
    stdin.encoding = cp437
    stdout.encoding = cp437
    sun.arch.data.model = 64
    sun.boot.library.path = c:\Program Files\Eclipse Adoptium\jdk-25.0.2.10-hotspot\bin
    sun.cpu.endian = little
    sun.cpu.isalist = amd64
    sun.io.unicode.encoding = UnicodeLittle
    sun.java.launcher = SUN_STANDARD
    sun.jnu.encoding = Cp1252
    sun.management.compiler = HotSpot 64-Bit Tiered Compilers
    sun.os.patch.level =
    user.country = US
    user.dir = C:\temp\canonical-path-test
    user.home = C:\Users\bodewig
    user.language = en
    user.script =
    user.variant =

openjdk version "25.0.2" 2026-01-20 LTS
OpenJDK Runtime Environment Temurin-25.0.2+10 (build 25.0.2+10-LTS)
OpenJDK 64-Bit Server VM Temurin-25.0.2+10 (build 25.0.2+10-LTS, mixed mode, sharing)


A DESCRIPTION OF THE PROBLEM :
When running java from within a directory that is a symbolic link the current working directory as reflected by the File constructor or the user.dir system property resolves the symlink on Linux but does not on Windows.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
on Linux

$ mkdir -p /tmp/cwd-test/normal
/tmp/canonical-path-test$ cd /tmp/cwd-test
/tmp/cwd-test$ ln -s normal symlink
# copy WhereAmI to /tmp/cwd-test
$ /usr/lib/jvm/java-25-openjdk-amd64/bin/javac WhereAmI.java
$ cd symlink
# run WhereAmI

On Windows

Windows:

>cd \Temp

C:\temp>mkdir cwd-test

C:\temp>cd cwd-test

C:\temp\cwd-test>mkdir normal

C:\temp\cwd-test>mklink /D symlink c:\temp\cwd-test\normal
symbolic link created for symlink <<===>> c:\temp\cwd-test\normal

C:\temp\cwd-test>mklink /J junction c:\temp\cwd-test\normal
Junction created for junction <<===>> c:\temp\cwd-test\normal

# copy WhereAmI to C:\temp\cwd-test

C:\temp\cwd-test>"c:\Program Files\Eclipse Adoptium\jdk-25.0.2.10-hotspot\bin\javac.exe" WhereAmI.java

C:\temp\cwd-test> cd symlink
# run WhereAmI
C:\temp\cwd-test\symlink> cd ..\junction
# run WhereAmI


---------- BEGIN SOURCE ----------
import java.io.*;

public class WhereAmI {

    public static void main(String[] args) {
        System.err.println("user.dir is " + System.getProperty("user.dir"));
        System.err.println("Current dir is " + new File(".").getAbsolutePath());
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
never trust user.dir or use the single-String arg File constructor but rather invoke getCanonicalPath on whatever user.dir returns and specify it as base directory explicitly, I guess.