chore: sync CLI command reference (v0.91.0)

[github-actions]

Automated sync of _data/cli/command-reference.md from the latest
keboola/cli release.
The diff is effectively the CLI changelog since the last sync.

Freshness check: FINDINGS — docs mention commands/flags the CLI no longer has

CLI reference gate — 267 commands (v0.91.0) vs 360 pages

ai/mcp-server/index.md:582  kbagent tool
  ✗ unknown command `kbagent tool` (did you mean `kbagent org`?)

cli/commands.md:72  tool
  ✗ unknown command group `tool`

cli/for-agents.md:63  kbagent tool
  ✗ unknown command `kbagent tool` (did you mean `kbagent org`?)

cli/troubleshooting.md:13  kbagent doctor --fix
  ✗ unknown flag `--fix` for `kbagent doctor`

cli/troubleshooting.md:123  kbagent doctor --fix
  ✗ unknown flag `--fix` for `kbagent doctor`
──────────────────────────────────────────────────
5 finding(s).

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Project	Deployment	Actions	Updated (UTC)
connection-docs	Ready	Preview	Aug 27, 2026 8:20am

[linear-code]

PRDCT-559