Upgrade libsodium to 1.0.18-FINAL for CVE-2025-69277 [Medium]

[Kanishk-Bansal]

Merge Checklist

All boxes should be checked before merging the PR (just tick any boxes which don't apply to this PR)

• The toolchain has been rebuilt successfully (or no changes were made to it)
• The toolchain/worker package manifests are up-to-date
• Any updated packages successfully build (or no packages were changed)
• Packages depending on static components modified in this PR (Golang, *-static subpackages, etc.) have had their Release tag incremented.
• Package tests (%check section) have been verified with RUN_CHECK=y for existing SPEC files, or added to new SPEC files
• All package sources are available
• cgmanifest files are up-to-date and sorted (./cgmanifest.json, ./toolkit/scripts/toolchain/cgmanifest.json, .github/workflows/cgmanifest.json)
• LICENSE-MAP files are up-to-date (./LICENSES-AND-NOTICES/SPECS/data/licenses.json, ./LICENSES-AND-NOTICES/SPECS/LICENSES-MAP.md, ./LICENSES-AND-NOTICES/SPECS/LICENSE-EXCEPTIONS.PHOTON)
• All source files have up-to-date hashes in the *.signatures.json files
• sudo make go-tidy-all and sudo make go-test-coverage pass
• Documentation has been updated to match any changes to the build system
• Ready to merge

---

Summary

What does the PR accomplish, why was it needed?

• Upgrade libsodium for CVE-2025-69277 (MEDIUM).

Change Log

• CVE-2025-69277

Does this affect the toolchain?

NO

Associated issues

• N/A

Links to CVEs

• https://nvd.nist.gov/vuln/detail/CVE-2025-69277

Test Methodology

• Pipeline build id: Buddy Build URL

[Kanishk-Bansal]

Source Tarball - https://dev.azure.com/mariner-org/mariner/_build/results?buildId=1019826&view=results
Buddy Build - https://dev.azure.com/mariner-org/mariner/_build/results?buildId=1020127&view=results
jedisct1/libsodium@5106e05 Commit shows that CVE fix has been taken to 1.0.18-FINAL tarball which was released with the security fix after 1.0.18 as a pointer release.
Updated the tarball and added autoreconf -fiv as previously the build was failing with the error

`time="2026-01-06T17:17:18Z" level=debug msg="+ ./configure --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-silent-rules --disable-opt"

time="2026-01-06T17:17:18Z" level=debug msg="/var/tmp/rpm-tmp.0cHz2U: line 49: ./configure: No such file or directory"
`

[mayankfz]

changes looks fine