[Bug?]: yarn up replaces catalog: references in package.json instead of updating the catalog

[emiliosheinz]

Self-service

• I'd be willing to implement a fix

Describe the bug

We are using Yarn catalogs to centralize dependency versions in a monorepo. The expected behavior is that upgrade commands update the catalog entries (in .yarnrc.yml) rather than rewriting package.json dependencies that use the catalog: protocol.

However, running yarn up with explicit versions breaks this expectation.

To reproduce

Given a catalog like:

catalog:
  react: 19.2.1

And a workspace package using:

{
  "dependencies": {
    "react": "catalog:"
  }
}

Running:

yarn up react@19.2.4

Rewrites package.json entries to the following:**

"react": "19.2.4"

Instead, the catalog entry should be updated, and the package.json should remain unchanged.

Environment

System:
  OS: macOS 26.3
  CPU: (14) arm64 Apple M4 Max
Binaries:
  Node: 22.18.0 - /private/var/folders/c2/r9vhzjgn15b5b5xcb6krf4th0000gp/T/xfs-9ca2a751/node
  Yarn: 4.12.0 - /private/var/folders/c2/r9vhzjgn15b5b5xcb6krf4th0000gp/T/xfs-9ca2a751/yarn
  npm: 10.9.3 - /Users/spoke/.volta/tools/image/node/22.18.0/bin/npm

Related issues

• [Bug?]: Dependencies from catalog: are not upgraded using upgrade-interactive #6951
• [Feature] Support catalog: protocol in yarn add #7081