fix(core): keep glob/grep permission metadata JSON-encodable

[Enough1122]

Issue for this PR

Closes #37650

Type of change

• Bug fix

What does this PR do?

Pending glob and grep permissions store absent optional tool inputs (path, include, limit) as undefined inside JSON permission metadata, so when session.permission.list encodes its response, schema validation fails with Expected JSON value, got undefined.

This adds a small jsonMetadata helper in packages/core/src/tool/metadata.ts that omits undefined fields, and builds the glob/grep permission metadata through it: absent optional inputs are simply left out of the record, so permission listing stays schema-valid whether or not the model supplied them.

How did you verify your code works?

• New unit tests in packages/core/test/tool-permission-metadata.test.ts cover the all-optional-absent case from the issue, the fully-populated case, and the mixed path-only case: 3 pass.
• Existing related suites still pass: tool-bash, tool-edit, filesystem/search → 22 pass.
• bun run typecheck clean in @opencode-ai/core and across the monorepo.

Screenshots / recordings

Not a UI change.

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR

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[github-actions]

The following comment was made by an LLM, it may be inaccurate:

Potential duplicate PRs found:

1. PR fix(core): omit absent optional fields from glob and grep permission metadata #40852: "fix(core): omit absent optional fields from glob and grep permission metadata"

   • fix(core): omit absent optional fields from glob and grep permission metadata #40852
   • This appears to address the exact same issue—omitting undefined optional fields from glob/grep permission metadata to maintain JSON schema validity.

2. PR fix(opencode): drop undefined from v1 permission metadata #38918: "fix(opencode): drop undefined from v1 permission metadata"

   • fix(opencode): drop undefined from v1 permission metadata #38918
   • This handles a related problem of removing undefined values from permission metadata encoding, though focused on v1.

Why they're related: Both PR #40852 and the current PR #44375 target the same core problem: preventing undefined values in glob/grep permission metadata JSON encoding to satisfy schema validation. You should review whether #40852 was already merged and if so, whether the current PR is redundant.

[github-actions]

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