docs: document gh_api sentinel contract and gh_api_paginate across all docs (#27)

- lib/github-common.sh: rewrite # Provides: header block — fix scrambled
  layout, add get_repo_page_count, document __404__/__422__ sentinel
  contract on gh_api, and note gh_api_paginate empty-output behaviour
- README.md: add configure_gh_auth to its own Auth helpers section;
  add gh_api_paginate to API helpers; clarify gh_api sentinel contract;
  move validate_slug to Validation section
- AGENTS.md: update gh_api and gh_api_paginate table rows to describe
  sentinel contract; add sentinel note to Rate limiting section
- copilot-instructions.md: update gh_api rate-limiting bullet to include
  sentinel contract; update github-dockerfile-discovery description to
  document both gh_api call sites' sentinel handling; add gh_api_paginate
  row to maintenance matrix

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: locus313

.github/copilot-instructions.md

@@ -101,7 +101,7 @@ For enterprise-level org iteration (GraphQL), use cursor-based pagination — se
 Rate limiting delays are calibrated per operation type:
 - **Repo-level operations** (permission grants, archival): `sleep 5` between each repository.
 - **Code search** (`github-dockerfile-discovery`): configurable via `SEARCH_SLEEP` (default 2 s) and `CONTENT_SLEEP` (default 1 s).
-- **gh_api helper** (lib): auto-retries up to 5 times on HTTP 403/429, sleeping 60 s before each retry.
+- **gh_api helper** (lib): auto-retries up to 5 times on HTTP 403/429, sleeping 60 s before each retry. Returns the literal string `__404__` or `__422__` (exit 0) for those HTTP statuses instead of failing — every caller must check for these sentinels before passing the result to `jq`. `gh_api_paginate` returns silently with empty output on 404/422.
 
 ### Authentication Headers
 
@@ -161,7 +161,7 @@ Dismisses open Dependabot, code-scanning, and secret-scanning alerts on all arch
 
 ### `github-dockerfile-discovery`
 
-Uses GitHub code-search API to find Dockerfiles across all enterprise orgs, then fetches and parses each file to extract `FROM` instructions (including multi-stage builds). Produces three timestamped reports in `REPORT_DIR`: a detail CSV, a summary CSV, and a plain-text summary. Supports `ORGS` override, `ORG_FILTER`/`ORG_EXCLUDE` regex filters (validated as syntactically correct ERE before use), and configurable sleep intervals (`SEARCH_SLEEP`, `CONTENT_SLEEP`).
+Uses GitHub code-search API to find Dockerfiles across all enterprise orgs, then fetches and parses each file to extract `FROM` instructions (including multi-stage builds). Produces three timestamped reports in `REPORT_DIR`: a detail CSV, a summary CSV, and a plain-text summary. Supports `ORGS` override, `ORG_FILTER`/`ORG_EXCLUDE` regex filters (validated as syntactically correct ERE before use), and configurable sleep intervals (`SEARCH_SLEEP`, `CONTENT_SLEEP`). Both `gh_api` call sites handle sentinels: `__422__` or `__404__` on the code-search endpoint skips that org with a warning; `__404__` or `__422__` on the file-contents endpoint skips that individual file.
 
 ### `github-enable-issues`
 
@@ -270,6 +270,7 @@ When you change one of these files, you must also update the files in the "Also
 |------------------|-------------|
 | `lib/github-common.sh` — any public function signature or behaviour | All 18 scripts that source it; verify each caller still passes the right arguments. Check with: `grep -r "github-common" . --include="*.sh"` |
 | `lib/github-common.sh` — add a new helper function | `AGENTS.md` shared library table; `README.md` if the function affects usage |
+| `gh_api_paginate` signature or pagination behaviour | `github-repo-permissions-report.sh` (3 call sites), `github-copilot-report.sh` (`fetch_seats`) — both pipe output through `jq -s '.'` and depend on the `jq_filter`/`api_version` parameter order |
 | Any script's required env vars | That script's `# ===` header comment; the corresponding README.md section's env var table; that script's `action.yml` inputs (add/remove required inputs to match) |
 | Any script's optional env vars or defaults | Same as above; update the `action.yml` optional inputs and their defaults |
 | Any script's `--dry-run` or CLI flag behaviour | README.md usage example for that script; that script's `action.yml` inputs and `run:` step flag construction |

AGENTS.md

@@ -145,8 +145,8 @@ Always use `SCRIPT_DIR` to build the path to `lib/github-common.sh`. The library
 | `configure_gh_auth [scope_hint]` | Bridge GITHUB_TOKEN→GH_TOKEN or verify gh auth session |
 | `validate_github_token [bearer]` | Verify GITHUB_TOKEN via /user endpoint |
 | `validate_slug <value> <label>` | Reject values with non-alphanumeric/hyphen/underscore chars |
-| `gh_api <path> [curl args...]` | Bearer-auth REST helper with 5-retry rate-limit handling |
-| `gh_api_paginate <path> [filter] [version]` | Paginated REST helper, follows Link headers, streams items |
+| `gh_api <path> [curl args...]` | Bearer-auth REST helper with 5-retry rate-limit handling; returns literal `__404__` or `__422__` for those HTTP statuses — callers must check for these sentinels |
+| `gh_api_paginate <path> [filter] [version]` | Paginated REST helper, follows Link headers, streams items; returns silently with empty output on 404/422 |
 | `get_enterprise_orgs` | Three-tier enterprise org resolver (REST → GraphQL → /user/orgs) |
 | `get_repo_page_count <url>` | Returns total pages for a paginated endpoint |
 
@@ -172,6 +172,7 @@ done
 - Repo-level operations (permission grants, archival): `sleep 5` between each repo
 - Code search: configurable `SEARCH_SLEEP` (default 2s) and `CONTENT_SLEEP` (default 1s)
 - `gh_api` auto-retries on HTTP 403/429 with 60s sleep
+- `gh_api` returns the literal string `__404__` or `__422__` (exit 0) for those HTTP statuses — callers must check for these sentinels before passing output to `jq`
 
 ---
 

README.md

@@ -854,11 +854,15 @@ All scripts can leverage a shared utility library for common operations like val
 - `require_command <cmd> [hint]` — Exit if command is not in PATH
 - `validate_token <VAR_NAME> [bearer]` — Validate GitHub token by calling `/user` endpoint
 - `validate_github_token [bearer]` — Convenience wrapper for `GITHUB_TOKEN` validation
+- `validate_slug <value> <label>` — Exit if value contains characters other than alphanumeric, hyphen, or underscore
+
+**Auth helpers:**
+- `configure_gh_auth [scope_hint]` — Bridge `GITHUB_TOKEN→GH_TOKEN` for scripts that use the `gh` CLI, or verify an active `gh` auth session if no token is set
 
 **API helpers:**
 - `get_repo_page_count <url>` — Get total page count from paginated REST endpoint
-- `validate_slug <value> <label>` — Exit if value contains characters other than alphanumeric, hyphen, or underscore
-- `gh_api <path|url> [curl args...]` — Bearer-auth REST helper with automatic rate-limit retry (up to 5 attempts); returns `__404__` / `__422__` for those status codes instead of failing
+- `gh_api <path|url> [curl args...]` — Bearer-auth REST helper with automatic rate-limit retry (up to 5 attempts); returns the literal string `__404__` or `__422__` (exit 0) for those status codes — callers must check for these sentinels before passing the result to `jq`
+- `gh_api_paginate <path> [jq_filter] [api_version]` — Paginated REST helper that follows `Link` headers and streams items through `jq_filter` (default `.[]`); silently returns empty output on 404/422; pipe through `jq -s '.'` to collect all items as an array
 - `_paginate_orgs_endpoint <jq_filter> <url_template>` — Page through an org-list REST endpoint, printing one login per line; use `PAGE` as a placeholder in the URL template
 - `_graphql_enterprise_orgs` — Cursor-based GraphQL pagination for all orgs in `ENTERPRISE`; prints one login per line
 - `get_enterprise_orgs` — Three-tier enterprise org resolver: tries REST `/enterprises/{slug}/organizations`, falls back to GraphQL, then falls back to `/user/orgs`

lib/github-common.sh

@@ -12,22 +12,26 @@
 #
 # Provides:
 #   print_status / print_success / print_warning / print_error
-#   require_env_var <VAR> [description]  — exit if variable is unset/empty
-#   require_command <cmd>                — exit if command not found
-#   configure_gh_auth [scope_hint]       — bridge GITHUB_TOKEN→GH_TOKEN or verify gh session
-#   validate_github_token [bearer]       — verify token via /user endpoint
+#   require_env_var <VAR> [description]       — exit if variable is unset/empty
+#   require_command <cmd>                     — exit if command not found
+#   configure_gh_auth [scope_hint]            — bridge GITHUB_TOKEN→GH_TOKEN or verify gh session
+#   validate_github_token [bearer]            — verify GITHUB_TOKEN via /user endpoint
+#   validate_token <VAR_NAME>                 — verify a secondary token variable
+#   validate_slug <value> [label]             — exit if value contains unsafe chars
+#   gh_api <path|url> [curl args...]          — Bearer-auth REST helper with retry;
+#                                               returns "__404__"/"__422__" (exit 0) for those codes
+#   gh_api_paginate <path> [filter] [version] — paginated REST, follows Link headers;
+#                                               silently returns empty output on 404/422
+#   get_repo_page_count <url>                 — total page count for a paginated REST endpoint
+#   _paginate_orgs_endpoint <filter> <url_tpl> — page through an org list (internal)
+#   _graphql_enterprise_orgs                  — GraphQL cursor-based enterprise orgs (internal)
+#   get_enterprise_orgs                       — three-tier enterprise org resolver
 #
 # Token auto-resolution (at source time):
 #   If GITHUB_TOKEN is unset and gh CLI is available, the token is automatically
 #   resolved from the active gh auth session so curl-based scripts work with
-#   either a GITHUB_TOKEN env var or a gh CLI session.
-#   validate_token <VAR_NAME>            — verify a secondary token variable
-#   validate_slug <value> [label]        — exit if value contains unsafe chars
-#   gh_api <path|url> [curl args...]     — Bearer-auth REST helper with retry
-#   gh_api_paginate <path> [filter] [version] — paginated REST, follows Link headers
-#   _paginate_orgs_endpoint <filter> <url_tpl>  — page through an org list
-#   _graphql_enterprise_orgs             — GraphQL cursor-based enterprise orgs
-#   get_enterprise_orgs                  — three-tier enterprise org resolver
+#   either a GITHUB_TOKEN env var or a gh CLI session. GH_TOKEN is also kept
+#   in sync with GITHUB_TOKEN so gh CLI calls use the same credential.
 # =============================================================================
 
 ###