A zero-error result means the supported mechanical checks found no errors. It does not mean a paper is correct, every citation is present or every equation survived conversion. Keeping that boundary explicit makes the report more useful.
Code is not prose
The inspector parses Markdown into an abstract syntax tree using mdast-util-from-markdown. Fenced code, indented code and inline code are excluded from heading and link diagnostics. A tutorial that quotes  inside code therefore does not need that image. Dollar signs receive no diagnosis at all: this tool does not validate math delimiters, so a price or shell variable is not treated as a broken equation.
An unclosed fenced code block is a supported error. CommonMark itself permits a fence to run to end-of-file; this research-workflow check deliberately flags it as a possible accidental capture of later prose. Review the source before changing it.
Paths are local, not a crawl
Relative attachment paths resolve against the Markdown file’s directory, not your shell’s working directory. Percent-encoded names are decoded. URL fragments and query strings are removed for the filesystem check. Absolute filesystem paths are also interpreted by the local filesystem; remote schemes, protocol-relative URLs and fragment-only links are skipped. The tool never requests an external address. It does not validate image contents or heading-anchor targets.
References and exit codes
Defined reference links use the parser’s definitions. Undefined explicit forms such as [Dataset][data] are reported from text nodes. Undefined shortcut references such as [Dataset] are not checked, because ordinary bracketed prose has the same shape. Complex escaped bracket constructions can require manual review.
node src/cli.js paper.md --json # 0: no errors (warnings may remain) # 1: structural errors found # 2: invocation or file-read problem
A local research script can stop on code 1 while treating a heading jump as a warning. Run the bundled tests with npm test to see cases for fenced headings, inline links, Unicode filenames and real file-path decisions. The checker is read-only; it never “fixes” the source to make its report green.