docs: add CLI changelog entry for v0.99.0

[factory-droid]

Adds changelog entry for CLI v0.99.0 (April 10 release).

New features

• Incremental wiki refreshes
• Themed mermaid diagram colors
• Deep Wiki search and exports (app)

Bug fixes

• Theme background override, BYOK base URL switching, context model inheritance, spec editor terminal handoff, MCP auth cancellation, tool result display, custom model stability, directory not found error (app), BYOK usage limits (app), ghost tool calls, chat input (app), computer terminal (app), machine config modal (app), reasoning and model selection (app)