v0.1.0

Added

• GitHub Action and pharn-ci check CLI.

• Diff coverage: the share of lines added in the change that the coverage report (lcov or
  Cobertura XML) marks as executed, with an optional, inclusive threshold gate (threshold input,
  --threshold, coverage.threshold).

• Agent setup inventory: the tracked agent setup files of Claude Code, Cursor, GitHub Copilot,
  Codex, Gemini, Windsurf, Cline and MCP, listed by kind and never read. The kinds are claude-md,
  claude-local-md, agents-md, gemini-md, claude-settings, claude-settings-local,
  claude-skill, claude-hook, claude-agent, claude-command, cursor-rules, cursor-mcp,
  copilot-instructions, copilot-instructions-scoped, copilot-agents, copilot-prompts,
  vscode-mcp, codex-config, windsurf-rules, cline-rules and mcp-config, plus, for Aider,
  Continue, Roo Code, Amazon Q Developer, Junie, Zed, Augment, Kiro, Goose, OpenCode and Gemini CLI
  and for .claude/rules/, claude-rule, aider-config, conventions-md, continue-rules,
  roo-rules, amazonq-rules, junie-guidelines, zed-rules, augment-rules, kiro-steering,
  goosehints, opencode-config and gemini-settings. .mcp.json, .claude/ files and
  .cursor/rules/ are found in nested directories, and the more specific directory rule wins over
  a file-name rule.

• Report v1: optional agentSetup.summary (counts per kind and the tools involved), and an
  Agent setup: N files · tools line in the markdown, with the table collapsed above 25 files.

• Report v1 (schema/report.v1.json), the stable JSON output, with message codes
  DIFF_COVERAGE_BELOW_THRESHOLD, DIFF_COVERAGE_UNGATED, NO_COVERABLE_CHANGES,
  COVERAGE_FILE_MISSING, COVERAGE_FILE_EMPTY, COVERAGE_FORMAT_UNSUPPORTED,
  DIFF_UNAVAILABLE and NO_AGENT_SETUP_FILES.

• One sticky PR comment and a job summary; on fork PRs, where the token cannot comment, the job
  summary only.

• .pharn/ci.yml config file, overridden by Action inputs and CLI flags.

• Coverage exclusions: glob patterns (*, **, ?) from coverage.exclude, the CLI's repeatable
  --exclude <glob> and the Action's exclude input, merged (their union applies), leave matching
  changed files out of diff coverage. The report gains the optional diffCoverage.excludedFiles
  field, and the comment an "Excluded" summary listing them.

• Cobertura XML coverage parsing in core, read by the CLI and the Action.

• Coverage format selection: the coverage-format Action input, the --coverage-format CLI flag
  and coverage.format in .pharn/ci.yml take lcov, cobertura or auto. The flag or input
  wins over the config file.

• auto is the default: the format is detected from the first 1 KiB of the file, and the CLI
  (stderr) and the Action (log) print which format was used, for example
  coverage: cobertura (auto-detected). Clover and JaCoCo native XML are not supported.

• Message code COVERAGE_FORMAT_UNSUPPORTED: under auto, a coverage file that is neither lcov
  nor Cobertura XML is an error with a threshold, a warning without.

• Report v1: optional diffCoverage.format (lcov or cobertura), the format the report was
  read as.

• COVERAGE_LINES_SKIPPED (info): malformed lcov DA records and Cobertura <line> elements that were skipped while reading the coverage files are now counted, and the report says how many (a count only, no line numbers or file names). The verdict and the diff coverage numbers do not change, and reports that end before diff coverage is computed do not carry the message.

• Coverage auto-discovery: with no coverage-file input, no --coverage flag and no coverage.file, the Action and the CLI look for the coverage report at coverage/lcov.info, lcov.info, coverage.xml, coverage/cobertura-coverage.xml and **/coverage.cobertura.xml, and print coverage: <path> (auto-discovered) for each file they read. More than one kind found is an error asking you to set the path; none found is a COVERAGE_FILE_MISSING message (previously a usage error). Complete workflows for vitest, jest, pytest, .NET and cargo are in examples/workflows/.

• Expected agent tools: setup.expect in .pharn/ci.yml, the expect-agent-setup Action input and the CLI's --expect-agent-setup flag (repeatable) name agent tools (for example claude-code, cursor) that should have a setup file. Any tool no setup file configures is listed in the new agentSetup.missing field and reported as AGENT_SETUP_EXPECTED_MISSING (warn, or error when agent setup is required). A repo that expects nothing sees no change.

• AGENT_SETUP_FILE_EMPTY (warn): a listed agent setup file that is empty (size 0 in HEAD, from git ls-tree -r -l) is reported with the first path, and stays in the inventory. When git ls-tree fails, none is reported (the CLI notes it on stderr, the Action warns). Because it is a warning, the verdict of a repo with an empty CLAUDE.md changes from pass to warn.

• TEST_FILES_DELETED (info): the change deletes a test file, or renames one to a name that is not a test file
  (F-21). The message names up to five of them; the verdict is unchanged. Test files are recognized by name
  (.test./.spec. in the basename, or a test, tests or __tests__ directory).

• Agent setup inventory covers more tools (F-11): 13 new setup kinds, claude-rule (.claude/rules/), aider-config, conventions-md, continue-rules, roo-rules, amazonq-rules, junie-guidelines, zed-rules, augment-rules, kiro-steering, goosehints, opencode-config and gemini-settings, so the files of Aider, Continue, Roo Code, Amazon Q Developer, Junie, Zed, Augment, Kiro, Goose, OpenCode and Gemini CLI are listed. agents-md is now also credited to amp, jules, opencode and zed, and agentSetup.summary.tools in Report v1 accepts new tool names within v1 (a lowercase name pattern replaces the closed list).

• PR-number mode: the pr-number and head-sha Action inputs let pharn-ci measure and comment on a
  pull request from a workflow_run or workflow_dispatch run, with no PR code checked out. The PR,
  its diff and its file list come from the GitHub API (two new read-only calls: get a pull request,
  get a git tree), pr-number is validated, and head-sha is checked against the PR head. The README
  documents the two-workflow pattern for comments on fork PRs.

• Three warn-level messages for a change that touches the inputs of its own grade: CONFIG_CHANGED_IN_DIFF (the diff edits the pharn-ci config in use or a file under .github/workflows/), COVERAGE_FILE_TRACKED (the coverage file is a tracked file, so the change can supply its own numbers) and DIFF_BINARY_COVERED_FILE (the diff shows a covered source file as binary, e.g. through -diff in .gitattributes, so its added lines were not measured). They lift a pass to warn and never fail the check.

• Several coverage files and globs: the coverage-file Action input takes one entry per line, the CLI's --coverage flag is repeatable and coverage.file in .pharn/ci.yml can be a list. Each entry is a path or a glob (*, **, ?, relative to the workspace, the current directory or the repo root), so TestResults/**/coverage.cobertura.xml and packages/*/coverage/lcov.info work. The files are merged with hit counts summed; auto detects the format of each file. A glob that finds nothing is COVERAGE_FILE_MISSING; a walk stops at 1,000 matched files or 100,000 visited entries, never follows a symbolic link and skips .git and node_modules unless named.

• Require agent setup: the require-agent-setup Action input, the CLI's --require-agent-setup flag and setup.require in .pharn/ci.yml (off by default) make NO_AGENT_SETUP_FILES an error and the verdict fail when the repo has no agent setup files.

• DIFF_COVERAGE_UNGATED (info): diff coverage was measured, with its percent in the text, but no
  threshold gates it (none is set, or it is 0). Before, an ungated run passed with no message.

• Data handling section in SECURITY.md, linked from the README's Safety model: what the Action reads, what it sends to your GitHub API, what lands in the PR comment, job summary, step log and report.json, and that nothing is sent to Pharn.

• The rendered report (PR comment, job summary, CLI markdown) adds a one-line hint under each message
  saying how to fix it, and says what is missing (typically AGENTS.md or CLAUDE.md) when no agent
  setup files are found. Message text in report.json is unchanged.

• coverage.exclude in .pharn/ci.yml can be written as a one-line flow list, e.g.
  exclude: ["**", "dist/**"], which used to stop the check with exit code 2.

• Coverage root: coverage.root in .pharn/ci.yml, the coverage-root Action input and the CLI's --coverage-root flag name the repo-relative directory that relative coverage paths start from, so a package-relative lcov or Cobertura report in a monorepo is measured at the right files. Absolute paths are never remapped.

• COVERAGE_PATHS_PARTIALLY_UNMATCHED (info): some of the coverage report's file paths are not tracked files, so their coverage is not used. The verdict is unchanged. The fixtures/golden and fixtures/golden-cobertura reports gain this message.

Changed

• When more than one coverage file is read (a glob, a list, or several --coverage flags), the coverage: <format> (<how>) log line names its file: coverage: coverage/a.info: lcov (auto-detected). With one file the line is unchanged, and so is the (auto-discovered) line.
• The PR comment, job summary and CLI markdown now show the overview sentence in a GitHub alert under the verdict heading: [!CAUTION] for fail, [!WARNING] for warn, [!TIP] for pass. Report data and message text are unchanged.
• The PR comment, job summary and CLI markdown now show the pharn logo (a 48×48 image from the repository's raw main URL) above the verdict heading. Report data and message text are unchanged.
• The PR comment, job summary and CLI markdown have a new look. They open with a branded header (a verdict heading, a one-line overview and a summary table), use emoji section headings with counts, and collapse the changed-files and agent setup tables in <details> blocks (the changed-files block is open when diff coverage is below the threshold). They end with a footer naming the tool version, the report schema and the coverage format. Report data and message text are unchanged.
• Internal refactor: the CLI and the Action share their Node I/O (git, file reads, directory listing) and their coverage-file reading through a private workspace package, @pharn-ci/node-io. No user-visible change.
• Large inputs: the diff and lcov coverage are read line by line (F-15), so a diff is no longer limited by a 256 MiB buffer and lcov no longer by the longest string the engine can build (only one line that long still fails). The CLI and the Action stream git's output and the coverage file instead of reading them whole. Cobertura coverage and the config stay string-based. The limits of each input and what you see when one is passed are in docs/LIMITS.md §8 (Size limits).
• Versioning policy for 0.x (docs/RELEASING.md): Action inputs and outputs, CLI flags and message
  codes are never removed before 1.0; a renamed input keeps working under its old name, with a
  warning, for at least one minor release; a changed default ships only in a minor release and is
  listed here. The README status note and docs/LIMITS.md say the same.
• Agent setup inventory quality (F-10): .mcp.json, .claude/settings.json and .claude/settings.local.json count at the repo root only (a nested copy in a package or a test fixture is no longer listed); a dot-file or README under a directory kind (such as .claude/skills/x/.gitkeep or .github/agents/README.md) is not listed; and a path with a node_modules directory is never listed. Repos with such files see fewer files in agentSetup.files.
• A coverage entry (the coverage-file input, --coverage or coverage.file) containing [, ], { or } is
  rejected as unsupported glob syntax, even without * or ?. A literal coverage path with one of those characters
  is now a usage error.
• The rendered report lists messages before the agent setup inventory, and a file's uncovered-lines cell shows
  at most 20 ranges followed by …and N more. The Action fits an oversized PR comment (65,000 characters) or
  job summary (1 MiB) by rendering fewer table rows instead of cutting the end, so the verdict and messages
  stay visible; report.json keeps the full report.
• The diff coverage table lists files by coverage, lowest first (then by path), so the files that
  need tests stay visible when the table is cut at 50 rows; a cut table now points to the full list
  in report.json (the Action's report-path output, or --format json).
• .pharn/ci.yml errors for unsupported YAML now name the supported form (for example "use a block
  list").
• A coverage report whose paths match no tracked file is now COVERAGE_PATHS_UNMATCHED: an error, and
  the verdict fail, when a threshold is set (a warning without one), with the suggested coverage
  root when one can be found. Before, it passed as NO_COVERABLE_CHANGES. If your coverage paths are
  relative to a package directory, set coverage.root.
• DIFF_UNAVAILABLE is now an error, and the verdict fail, when a threshold is set (a warning
  without one), like a missing, empty or unrecognized coverage file. If a shallow checkout makes
  the diff unavailable, use actions/checkout with fetch-depth: 0 or rely on the GitHub API
  fallback.
• The diff coverage threshold is compared exactly against covered / coverable lines instead of the
  percent rounded to two decimals: 15,999 of 20,000 lines (79.995%) now fails a threshold of 80.
  A failing coverage that would round up to the threshold is shown rounded down (79.99%).
• Threshold 0 is documented as gating no percentage (reported with DIFF_COVERAGE_UNGATED); it
  still fails closed when coverage cannot be measured.
• The repository no longer tracks the maintainer's PHARN workflow install (pharn/,
  pharn.config.json, pharn.records.json and PHARN's own root LIMITS.md and THREAT-MODEL.md),
  so uses: pharn-dev/pharn-ci@... downloads about 5 MB less. pharn-ci's own threat model and
  limits are docs/THREAT-MODEL.md and docs/LIMITS.md.

Fixed

• CLI: a flag value that starts with - (for example --threshold -1 or --base -x) no longer fails with the misleading "Did you forget to specify the option argument?". The error (exit code 2, unchanged) now says the value must be written with =, for example --threshold=-1.
• Thresholds (--threshold, the threshold input and coverage.threshold) accept only plain decimal numbers from 0 to 100, such as 80 or 72.5. Exponent (1e2), hex (0x10), a sign, a bare or trailing dot (.5, 80.), Infinity, % and inner spaces were read as JavaScript numbers before and are now refused with the existing "must be a number between 0 and 100" error (exit 2).
• The README quick start no longer aborts for vitest: it says @vitest/coverage-v8 must be a dev dependency, and a
  new "Coverage per ecosystem" table shows the report and coverage-file for vitest, jest, pytest-cov, coverlet,
  cargo-llvm-cov, Go, and JaCoCo/Kover through a Cobertura converter.
• An lcov file whose SF records carry no DA lines (a crashed or truncated reporter) is now
  COVERAGE_FILE_EMPTY, as the Cobertura equivalent already was, instead of passing as
  NO_COVERABLE_CHANGES. lcov files without a valid DA line are left out of the coverage map.
• Docs: the quick start pins actions/checkout to a commit SHA; the Action reference gives the
  real threshold and base-ref defaults; the docs name Cobertura as untrusted input, the
  GET /user call, and the bundled transitive dependencies.
• The Action no longer crashes with a stack trace before running when github-token is empty. The
  token is used only when an API call is needed, so comment: false with a local diff works
  without one; otherwise the compare fallback reports DIFF_UNAVAILABLE and the comment step
  warns, as for any API failure. The github-token input now says pull-requests: write is
  needed only for the comment.
• Concurrent runs on one PR no longer leave two sticky comments: after creating its comment, the
  Action deletes newer duplicates of its own marker comment (only ones its own login wrote) and
  keeps updating the oldest. The README quick start now sets a per-PR concurrency group.
• Merge queue runs (merge_group) diff against merge_group.base_sha instead of always reporting
  DIFF_UNAVAILABLE.
• An explicit base-ref found neither in the checkout nor through the GitHub API now fails the
  step with an error naming the ref, instead of reporting DIFF_UNAVAILABLE.
• A config input naming a file that does not exist now fails the step with "config file not
  found", like the CLI's --config, instead of running with no config (and so without a threshold
  held only in the config). The input no longer has a default in action.yml; left empty, it reads
  .pharn/ci.yml when present, as before.
• The CLI lists tracked files from the repository root when run from a subdirectory, so coverage
  paths are compared with the same names wherever it runs. The agent setup inventory of a
  subdirectory run now covers the whole repo.
• With a GitHub App token, the sticky comment is now found and updated instead of re-posted on every
  run. Each workflow and job owns its own comment, marked by a <!-- pharn-ci scope: ... --> line
  under the marker, so sibling jobs no longer overwrite each other. Comments from earlier versions
  keep being updated, but a PR whose single comment was shared by two jobs gains one comment for
  the second job after the upgrade.
• When the Action falls back to the GitHub compare API and the response has no charset=utf-8 (it
  arrives as bytes) the diff is decoded as UTF-8, and a body that is not diff text (such as JSON)
  degrades to DIFF_UNAVAILABLE. Before, the step crashed with "text.split is not a function" and
  wrote no summary, report or outputs.
• A hung GitHub API or git call no longer stalls the Action for minutes per stage. Each API request
  is aborted after 30 s, and a 5xx, a network error or a rate limit asking for at most 60 s is retried
  once (honouring retry-after and x-ratelimit-reset); git calls in the Action and the CLI are
  killed after 2 minutes. The README example sets timeout-minutes: 5 on the step.
• Docs: the github-token input says the token is always used in pr-number mode; the README
  quick start's concurrency group falls back to github.ref, so merge-queue entries no longer
  cancel each other; the token-footprint bullet lists GET /user and the pr-number reads; and
  SECURITY.md's data handling names every message code that quotes a path, including the coverage
  report path quoted by COVERAGE_PATHS_UNMATCHED.

Security

• The PR comment cannot be altered through file names or message text: control characters in
  paths are replaced and HTML in messages is escaped.
• The sticky comment is matched by its author as well as its marker, so a comment someone else
  posted is never taken over.
• A base ref starting with - is rejected, and revisions reach git after --end-of-options.
• The config parser runs in linear time on hostile input.
• An empty or unparseable coverage file reports COVERAGE_FILE_EMPTY instead of passing.
• A pull_request_target run that checked out the base branch reports DIFF_UNAVAILABLE instead
  of passing.
• PR comments are capped below GitHub's size limit; the job summary keeps the full report.
• Repository protection: signed, linear, squash-merged main behind six required checks;
  immutable v* tags; every third-party action pinned to a commit SHA.
• SECURITY.md and docs/THREAT-MODEL.md state that pharn-ci has one maintainer: pull requests
  are merged with the main ruleset's admin bypass and releases are self-approved, so no second
  person reviews a change; they list what still enforces integrity and the plan for when a second
  maintainer joins. The threat model no longer says main takes only reviewed pull requests (F-18).
• A pull_request_target run that checked out the base branch no longer tells users to check out the
  PR head, which would run fork code with a write token. DIFF_UNAVAILABLE now says it cannot be
  measured safely and points to pull_request and SECURITY.md; the safe workflow_run pattern for
  comments on fork PRs is documented in the README.
• Cobertura path resolution no longer slows down quadratically on a crafted report with thousands
  of <source> entries and thousands of filenames (F-24). Results are unchanged, except that a
  relative filename starting with .. is now joined to at most the first 16 distinct sources.
• PR-controlled text in messages (the coverage path from .pharn/ci.yml, the base ref) no longer
  renders as links, images, emphasis or @mentions in the PR comment and job summary: markdown
  characters are escaped, @ cannot mention, and bare URLs are not autolinked. The report JSON
  keeps the message text unchanged.
• The Action's git rev-parse --verify lookup of the base ref now passes the revision after
  --end-of-options too, so every git call that takes a revision separates it from options.
• Release tags are documented as unsigned lightweight tags, with pinning the full commit SHA as the
  integrity control (README.md, SECURITY.md, docs/RELEASING.md). The packages/action/dist
  diff is no longer collapsed in pull requests (.gitattributes no longer marks it
  linguist-generated), and CI writes the changed dist files and the bundle's sha256 to the job
  summary of every pull request so reviewers see the shipped artifact change.