Running:
java -jar BuildTools.jar

BuildTools (latest) fails on Fedora 34, JDK 17, building Minecraft 1.18.1 (latest). The same BuildTools JAR works fine on Ubuntu. I don't understand how Ubuntu and Fedora could differ that much.

Adding a try-catch around org.spigotmc.builder.Builder.main(Builder.java:656) allows the build to complete without any obvious issues.

Loading BuildTools version: git-BuildTools-aff98e6-144 (#144)
Java Version: Java 17
Current Path: /home/totemo/minecraft/buildtools/.
git version 2.31.1
totemo
[email protected]
Picked up _JAVA_OPTIONS: -Djdk.net.URLClassPath.disableClassPathURLCheck=true
openjdk version "17.0.1" 2021-10-19
OpenJDK Runtime Environment 21.9 (build 17.0.1+12)
OpenJDK 64-Bit Server VM 21.9 (build 17.0.1+12, mixed mode, sharing)
Attempting to build version: 'latest' use --rev <version> to override
Found version
{
"name": "3403",
"description": "Jenkins build 3403",
"refs":

{ "BuildData": "f31eb04b918592f66c6edd17c9b5998383581ae5", "Bukkit": "13b723fcdb4faf6be001314cd980d3a5d6d27e0c", "CraftBukkit": "2e61a5f8eb81264737f9ad663eb9ed6616f3a19c", "Spigot": "f4ff00ffa451bd116cfbab3bd9d83b42e93904dd" }

,
"toolsVersion": 138,
"javaVersions": [61, 61]
}

... snip ...

Patching net/minecraft/advancements/Advancement.java
Patching net/minecraft/advancements/Advancements.java
Exception in thread "main" org.apache.commons.io.FileExistsException: File element in parameter 'destDir' already exists: 'CraftBukkit/src/main/java/net'
at org.apache.commons.io.FileUtils.requireAbsent(FileUtils.java:2587)
at org.apache.commons.io.FileUtils.moveDirectory(FileUtils.java:2222)
at org.spigotmc.builder.Builder.main(Builder.java:656)
at org.spigotmc.builder.Bootstrap.main(Bootstrap.java:27)