fix: shade third-party deps in codeflash-runtime JAR

[HeshamHM28]

Problem

The codeflash-runtime-1.0.0.jar is a fat JAR that bundles 2,000+ classes from Gson, Kryo, SLF4J, JaCoCo, etc. — all unshaded (no package relocation). When codeflash adds this JAR to a project's test classpath, it causes duplicate-class conflicts with the project's own dependencies.

Real-world impact: On OpenSearch, the bundled com.google.gson.* classes collide with Hadoop's Gson dependency, triggering OpenSearch's jarHell precommit check. This caused 602 build failures and 148 functions skipped.

Fix

Relocate all third-party packages under com.codeflash.shaded.* in both build systems:

Package	Shaded to
com.google.gson	com.codeflash.shaded.com.google.gson
com.esotericsoftware (Kryo)	com.codeflash.shaded.com.esotericsoftware
org.objenesis	com.codeflash.shaded.org.objenesis
org.slf4j	com.codeflash.shaded.org.slf4j
org.jacoco	com.codeflash.shaded.org.jacoco
org.objectweb.asm	com.codeflash.shaded.org.objectweb.asm

SQLite is left unshaded (native library loading depends on exact resource paths).

Also includes:

• Added jarHell and thirdPartyAudit to Gradle skip-validation init script as a safety net
• Added Gradle wrapper (8.12) to codeflash-java-runtime
• Synced JaCoCo dependencies to Gradle build (were Maven-only)

Verification

• Maven build + tests pass
• Gradle build + tests pass
• jar tf confirms zero unshaded third-party classes remain (except SQLite)
• com.codeflash.* public API is unchanged — shading is fully internal

🤖 Generated with Claude Code

[claude]

Claude finished @HeshamHM28's task in 1m 31s —— View job

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PR Review Summary

• Triage PR size → SMALL (42 additions, 3 deletions across 3 files)
• Lint and type check → all prek checks passed, no issues
• Resolve stale threads → none found
• Code review
• Duplicate detection

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Prek Checks

All ruff and format checks passed. No issues.

Code Review

Bug: Gradle and Maven relocation rules are out of sync

The latest commit ("fix: shade args4j and EMMA transitive deps") added org.kohsuke and com.vladium relocations to pom.xml but did not update build.gradle.kts with the same rules.

Current state:

Package	pom.xml	build.gradle.kts
org.objectweb.asm	✅ shaded	✅ shaded
com.google.gson	✅ shaded	✅ shaded
com.esotericsoftware	✅ shaded	✅ shaded
org.objenesis	✅ shaded	✅ shaded
org.slf4j	✅ shaded	✅ shaded
org.jacoco	✅ shaded	✅ shaded
org.kohsuke (args4j)	✅ shaded	❌ missing
com.vladium (EMMA)	✅ shaded	❌ missing

Any project using a Gradle-built JAR will still have org/kohsuke/args4j/ and com/vladium/emma/rt/ unshaded on the classpath. The two missing relocations should be added to build.gradle.kts:

relocate("org.kohsuke", "com.codeflash.shaded.org.kohsuke")
relocate("com.vladium", "com.codeflash.shaded.com.vladium")

Fix this →

Duplicate Detection

No duplicates detected.

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Last updated: 2026-03-31

[mashraf-222]

Two JaCoCo CLI transitive deps are still unshaded in the fat JAR:

• org/kohsuke/args4j/ (~30 classes) — old CLI parser, most projects use picocli/JCommander now
• com/vladium/emma/rt/ (2 classes) — dead EMMA coverage project

Low collision risk, but for completeness:

<relocation>
    <pattern>org.kohsuke</pattern>
    <shadedPattern>com.codeflash.shaded.org.kohsuke</shadedPattern>
</relocation>
<relocation>
    <pattern>com.vladium</pattern>
    <shadedPattern>com.codeflash.shaded.com.vladium</shadedPattern>
</relocation>