Lerna version from version lifecycle polluting global lerna execution

Expected Behavior

lerna version would automatically commit the changes or at least complete correctly.

Current Behavior

Running lerna version does update the version in the package.json but then immediately complains about those changes are unstaged and exits.

lerna version
lerna notice cli v3.16.4
lerna info current version 1.1.3
lerna info Looking for changed packages since v1.0.3
? Select a new version (currently 1.1.3) Patch (1.1.4)

Changes:
 - @me/packageA: 1.1.3 => 1.1.4
 - @me/packageB: 1.1.3 => 1.1.4

? Are you sure you want to create these versions? Yes
lerna info execute Skipping releases
lerna info lifecycle root@1.1.3~version: root@1.1.3

> root@1.1.3 version /Users/iMightyJun/Projects/Mitosis
> lerna version

lerna notice cli v3.16.4
lerna info current version 1.1.4
lerna info Looking for changed packages since v1.0.3
lerna ERR! EUNCOMMIT Working tree has uncommitted changes, please commit or remove the following changes before continuing:
lerna ERR! EUNCOMMIT  M lerna.json
lerna ERR! EUNCOMMIT  M packages/packageA/package.json
lerna ERR! EUNCOMMIT  M packages/packageB/package.json
lerna info lifecycle root@1.1.3~version: Failed to exec version script
lerna ERR! lifecycle "version" errored in "root", exiting 1

Possible Solution

lerna version should recognize it made those package.json changes and either stage these commits automatically or exit gracefully.

Steps to Reproduce (for bugs)

1. run lerna version
2. type yes

lerna.json

{
  "version": "1.1.4",
  "npmClient": "yarn",
  "useWorkspaces": true,
  "command": {
    "publish": {
      "message": "chore(release): publish %s"
    },
    "version": {
      "allowBranch": "master",
      "message": "chore(release): %s"
    },
    "run": {
      "npmClient": "yarn"
    }
  },
  "packages": [
    "packages/*"
  ]
}

lerna-debug.log

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Context

Your Environment

Executable	Version
lerna --version	v3.16.4
npm --version	6.9.0
yarn --version	1.17.0
node --version	v10.16.0

| OS | Version | | macOS Mojave| 10.14.5 | | NAME | VERSION |

[evocateur]

but the underlying problem is

You’re running lerna version with a version lifecycle in the root package.json. Don’t do that, and you’ll avoid this error.

In general, you should not name the scripts that you call lerna commands from (in the root package.json) “publish” or “version”, as these are significant names in npm-land.

I thought https://github.com/lerna/lerna/commit/089392d242b6326f4865f81a8083ea858ed4091b would have fixed this, but I guess I failed to account for folks who call lerna globally. PRs welcome.

[kkataev]

This issue just appeared on mac after reinstall lerna. Please, help)

Executable	Version
lerna --version	v3.16.4
npm --version	6.10.3
node --version	10.16.3