What

Closes the long-standing gap that bioassert cannot ask "does this file not contain X". Two additions, designed together:

1. A not comparator modifier. Any comparator can be prefixed with not (not contains, not matches, not starts, not ends). The string comparators previously had no negation (eq had ne, but starts/ends/contains/matches had nothing), which is why absence checks had to be pre-greped outside the tool.

2. A file.contents metric. The file-backed twin of text.value: it reads the whole body as a UTF-8 string and compares it with the string comparators. With the modifier, out.log file.contents not contains 'Exception' is the native replacement for a grep -v pre-step.

out.log       file.contents not contains 'Exception'   # PASS when the log has no Exception
reads.tsv     tsv.column.3.data.all not matches '^ERR'  # PASS when no data cell starts with ERR
ref.fasta     fasta.seq.0.name not starts 'chrUn'       # PASS when the first record is placed
output.bam    file.size not gt 1MB                      # accepted, equals lte 1MB

Key design decision

Negation is applied per comparison, not on the assertion's final result. For a scalar metric the two are identical, but for the whole-column aggregates they diverge:

• Negating the final result of column.N.all contains X gives the De Morgan dual "some cell lacks X".
• Negating the per-cell comparison gives "no cell contains X", the natural reading of column.N.all not contains X.

Baking negate into StringMatcher::is_match gets the per-cell form for free: the existing streaming check_column yields the correct "none" semantics with correct first-offender reporting (got line 3 = "NDA"), with no change to that code.

Blast radius

Comparator becomes an Operator plus a negate flag. Because every executor already calls compare / string_matcher / compare_string as methods, no executor call site changes, and because the comparator stays a single source-slice token on the AST (not contains), the report message renders the modifier verbatim with no formatting change. The real edits are the grammar's comparator rule, comparator.rs, the new src/file/contents/ module, dispatch registration, and docs.

Out of scope (deferred, recorded in the spec)

• Streaming file.lines.{any,none,all} for multi-gigabyte files (file.contents reads the body into memory, so it is scoped to log-sized text).
• Full boolean composition (and, or, grouped not).
• Comparator/metric coherence checking (not inherits the existing mis-pairing footgun).

Tests

• Unit: Comparator parse/compare/display under negation, StringMatcher negation for streaming, file.contents read and bounded summary, non-UTF-8 and missing-file errors.
• Integration (tests/negated_subcommand_test.rs): the grep-replacement PASS path, presence FAIL, negation-of-present-word FAIL, the per-cell "none" FAIL with first-offender reporting, the redundant numeric not, and the binary-file ERROR. Plus an all-passing run snapshot.
• Full suite: 355 passing, cargo fmt --check clean, cargo clippy --all-targets clean.

Design doc: specs/negated-comparators.md.

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