Sections

Every top-level key a settings file can declare, one row per section: the endpoints it drives, the fine-grained PAT permission it needs, what happens to the live resources the file does not declare, and the notes that matter when declaring it.

Section	Endpoints	PAT permission	Undeclared default	Notes
repository	PATCH repo, PUT topics, vulnerability-alerts, automated-security-fixes, private-vulnerability-reporting, lfs, immutable-releases, GraphQL RepositoryFeatures + UpdateRepositoryFeatures	Administration: write	untouched	Probot repository payload plus enable_* feature toggles; topics as string or list; enable_sponsorships and issue_creation_policy (all/collaborators_only) route through GraphQL - REST has no surface for them; declared fields only, undeclared siblings untouched
labels	labels CRUD	Issues: write	deleted (settable)	upsert by name (rename via new_name); the delete-by-default is Probot parity
rulesets	repo rulesets CRUD	Administration: write	kept (settable)	branch, tag, and push targets; short ref names auto-prefixed (staging -> refs/heads/staging); deletion stays an explicit opt-in
environments	environment listing + PUT environments + per-environment variables, secrets, deployment branch policies, deployment protection rules, and pins (GraphQL EnvironmentPins + EnvironmentPinsSnapshot + PinEnvironment + ReorderEnvironment)	Environments: write; declared deployment_branch_policies and deployment_protection_rules keys additionally need Actions: read and Administration: write	untouched	reviewers, wait timer, branch-policy flags; nested variables, secrets, deployment_branch_policies, and deployment_protection_rules keys reconcile per environment, each with its own _undeclared: knob (within a declared key, undeclared variables and branch-policy patterns are deleted; secrets and protection rules are kept); a pinned key pins the environment on the home page's deployments sidebar over GraphQL (declaration order sets the pin order, max 10 pins; environments without the key are never unpinned)
branches	protected-branch listing + classic branch protection + required-signatures sub-endpoint + app-by-slug actor lookup + GraphQL BranchProtectionRules + BranchProtectionRulesSnapshot + BranchProtectionRepository + BranchProtectionActorUser + BranchProtectionActorTeam + CreateBranchProtectionRule + UpdateBranchProtectionRule + DeleteBranchProtectionRule	Administration: write	untouched	protection: null removes protection; the protection PUT drops required_signatures, so declare it on any branch already carrying it; force_push_bypassers (users, org/team, app/slug) and required_deployments ride the GraphQL rule mutation; wildcard entries (release/*) reconcile entirely through GraphQL with a fixed key set; add Contents: read so check mode can tell a missing branch from an unprotected one
autolinks	autolinks CRUD	Administration: write	deleted (settable)	immutable upstream, so changed entries are replaced
actions	actions permissions + selected-actions + workflow token + access level + artifact/log retention + cache limits + OIDC subject claim + fork PR policies	Administration: write; the oidc_customization_sub key alone instead needs Actions: write	untouched	keys with their own sub-endpoint route there; everything else rides the base permissions PUT verbatim
actions_secrets	actions secrets list + public-key (read at apply) + sealed PUT + delete	Secrets: write	kept (settable)	{name, value: $NAME} sealed writes, re-sent every apply; existence-only checks, values unrecoverable
dependabot_secrets	dependabot secrets list + public-key (read at apply) + sealed PUT + delete	Dependabot secrets: write	kept (settable)	as actions_secrets, over the Dependabot secret store
codespaces_secrets	codespaces secrets list + public-key (read at apply) + sealed PUT + delete	Codespaces secrets: write	kept (settable)	as actions_secrets, over the Codespaces secret store
agents_secrets	agents secrets list + public-key (read at apply) + sealed PUT + delete	Agent secrets: write	kept (settable)	as actions_secrets, over the Copilot agents secret store
workflows	Actions workflows list, enable/disable	Actions: write	untouched	{path, state: active or disabled}; bare file names match .github/workflows/
check_suite_preferences	check-suites preferences PATCH (no read endpoint exists upstream)	Checks: write	untouched	per-app auto_trigger_checks toggles; write-only: check mode cannot verify them (one note, zero requests) and apply re-asserts them every run; the token owner must be a repository administrator
pages	POST/PUT/DELETE pages	Pages: write	untouched	build_type: workflow or legacy + source, cname, https_enforced, public (GHEC site visibility); pages: null disables the site
code_scanning_default_setup	code scanning default setup	Administration or Code scanning alerts: write	untouched	state, query_suite, languages; needs Advanced Security on private repositories
code_quality_setup	code-quality setup	Administration: write	untouched	state, languages, runner and AI-findings options; a 202 means GitHub rolls the change out in a configuration run; needs code quality available on the repository
collaborators	direct collaborators + pending invitations	Administration: write	deleted (settable)	invitations for new users, pending ones reconciled (stale permission updated, expired re-sent, undeclared cancelled); the repository owner is never touched
teams	org team repo permissions + repo team list	Members: read (org permission) + Administration: write	kept (settable)	org repos only, skipped with a notice on personal accounts; undeclared teams kept by default (_undeclared: delete revokes their direct access)
milestones	milestones	Issues: write	kept (settable)	upsert by title; deleting a milestone detaches it from every issue carrying it, which is why keep is the default
interaction_limits	interaction-limits + pulls creation-cap/bypass-list	Administration: write	untouched	re-arms the self-expiring limit every apply run; null clears it (base limit only); a 409 (org/user-level limit overrides) becomes a note; the PR creation cap is persistent (PATCHed only on divergence, 405 where unavailable) and its bypass logins reconcile add/remove
actions_variables	Actions variables CRUD	Variables: write	deleted (settable)	plain-text variables upserted by name (case-insensitive); values read back in full, so check mode diffs them exactly
agents_variables	Copilot agents variables CRUD	Agent variables: write	deleted (settable)	as actions_variables, over the Copilot agents variable store
webhooks	hooks CRUD + hook config sub-endpoint	Webhooks: write	kept (settable)	one hook per config.url, the natural key; config.secret takes a $NAME reference and is re-sent every run
custom_properties	GET/PATCH properties/values; probes GET /orgs/	Custom properties: write	kept (settable)	values of org-defined properties (definitions are org-scoped); org repos only, skipped with a notice on personal accounts; value: null unsets
deploy_keys	deploy keys list/create/delete	Administration: write	kept (settable)	matched by title; the declared material is a PUBLIC key; immutable upstream, so changed entries are replaced
secret_scanning_custom_patterns	secret-scanning custom patterns: paginated list + bulk POST + PATCH by id + bulk DELETE	Secret scanning alerts: write	kept (settable)	matched by name (immutable upstream); state and push_protection_enabled are not declarable; deletes always resolve alerts

The Undeclared default column

What happens to a live resource the settings file does not declare:

Value	Meaning
deleted (settable)	An undeclared resource is deleted on apply, so the declared list is the complete inventory.
kept (settable)	An undeclared resource is left in place; only declared entries are compared and written.
untouched	Undeclared top-level entries are neither compared nor changed; only declared keys are applied. A nested list inside a declared entry (an environment's variables, say) has its own default, named in the Notes cell.

(settable) means the wrapped _undeclared: form overrides the default per file. The undeclared policy covers the knob and how it layers in mode: render.

Where to read next

• Semantics: the model every section shares (stateless, declared-keys-only, convergent applies, loud failures).
• Forward compatibility: which sections pass payloads through verbatim and which are closed.
• Coverage: every row above expanded into its areas, one link per call, with the facts and caveats as notes, plus the gaps.