fix: correct admonition formatting and add missing bot permissions in docs

[adamrtalbot]

Summary

• Fix MkDocs admonition formatting across 4 doc files — content was missing the required 4-space indent, causing it to render outside the admonition box
• Convert GitHub > [!NOTE] syntax to MkDocs !!! note in api.md
• Fix code blocks in gallery.md (single backticks → triple backticks)
• Add missing bot permissions (reactions:write, files:write) to the setup guide
• Add <!-- prettier-ignore --> comments to protect admonition indentation from Prettier reformatting

Files changed

File	Change
docs/usage/guide.md	Fix 4 admonitions missing indentation
docs/index.md	Fix 1 admonition missing indentation
docs/examples/gallery.md	Fix admonition indent + code block backticks
docs/reference/api.md	Convert GitHub note syntax to MkDocs admonition
docs/getting-started/setup.md	Add reactions:write and files:write scopes

[claude]

PR Review

Summary: Doc formatting fixes + version bump to 0.5.0 + missing bot permissions.

Documentation ✅

• Admonition indentation fixes are correct (4-space indent required by MkDocs).
• <!-- prettier-ignore --> guards are a good safeguard to prevent regressions.
• GitHub > [!NOTE] → MkDocs !!! note conversion in api.md is correct.
• Code block fix in gallery.md (single backtick → triple backtick) is accurate.

Missing Bot Permissions ✅

• reactions:write and files:write added to setup guide with links to relevant sections — clear and actionable.

Examples ✅

• All example configs bumped to 0.5.0 consistently.

CHANGELOG ⚠️

• build.gradle was 0.4.1 before this PR, but the CHANGELOG jumps from 0.4.0 to 0.5.0 — 0.4.1 has no changelog entry and no version history line. If 0.4.1 was ever published to the Nextflow plugin registry, users on that version won't find it in the changelog.

Tests

No new tests needed — this is a documentation-only change.

Minor

No issues.