Structured output and fixes

ryni check . --output-format json

JSON output contains exactly one object on stdout, including for configuration or input errors. Argument-parsing errors are handled by Clap on stderr before a scan starts. There is no ANSI color or human summary in JSON output.

The schema has schema_version = 1 and these fields:

Field	Meaning
complete	False when any execution error prevented a complete scan. Lint findings alone do not make a scan incomplete.
files_discovered	Supported files admitted by discovery.
files_checked	Files successfully read and analyzed; individual target errors can still make the scan incomplete.
files_fixed	Files changed during this invocation. Findings describe the subsequent check.
diagnostics	Sorted findings with rule, severity, message, path, range, location, end_location, and fix.
errors	Execution failures with operation, path, and message.

Paths use forward slashes and are normally scan-root-relative for document findings. Startup/configuration/discovery errors can contain absolute paths. Non-UTF-8 paths are rendered lossily. Project-level findings use . as their path. All current findings have severity error.

range is null for a file-level finding, otherwise { "start": 0, "end": 10 } with half-open UTF-8 byte offsets. Locations are null or objects containing one-based line and Unicode scalar column. End locations are exclusive. Consumers must not interpret columns as bytes, terminal display cells or UTF-16 code units. Human messages may change; use the stable rule ID for automation.

A proposed fix has title, applicability (safe, unsafe or display-only), and edits. Each edit has a byte range and replacement string. A proposal does not mean the file has been changed. Schema consumers should tolerate additional object fields. Incompatible structural changes will increment the schema version.

Exit codes remain 0 for clean/empty scans, 1 for findings, and 2 for execution errors. Execution errors take precedence over findings. Phase timing output is opt-in on stderr and is not part of this JSON contract.

Applying fixes

ryni check . --fix
ryni check . --fix --unsafe-fixes

--fix applies only safe fixes. The first implemented fix is for skill-directory-name; it is unsafe, so it requires both flags. It sets the skill name to a valid containing-directory name and reserializes its frontmatter. This changes the skill identity and may remove YAML comments or alter formatting. The document body, BOM, and existing CRLF style are preserved. No safe fixes are currently offered by built-in rules. Display-only fixes are never applied.

Fixes are skipped for incomplete scans. For each affected file, Ryni verifies that its contents still match the analyzed snapshot, validates edit ranges, rejects overlapping edits, and checks that the resulting skill frontmatter parses. It writes through a temporary file, preserves permissions and replaces the destination. Individual files are replaced atomically; the whole repository is not one transaction. Avoid editing files concurrently with fix application.

Changed files are rechecked before output is produced. Remaining findings still cause exit code 1; application or recheck errors cause exit code 2.