feat(stream-c): kei-sage substrate — walk atoms/*.md + wikilink graph
Extends kei-sage with substrate-atom indexing layer per locked schema
§Graph / discovery contract.
New modules (all ≤ 200 LOC, Constructor Pattern):
- src/atom_parse.rs — frontmatter splitter, wikilink parser, id splitter
- src/atoms.rs — AtomKind + FromStr, AtomRecord, discover_atoms, resolve_wikilinks
- src/atom_index.rs — persists atoms as Units + atom_related edges into existing Store
- src/atom_cli.rs — 4 subcommand handlers
New CLI subcommands (default root ~/.claude/agents/_primitives/_rust):
- atoms-discover — walks atoms/*.md, prints table
- atoms-rank — PageRank over wikilink edges (composes w/ existing vault)
- atoms-related <atom-id> — BFS from atom
- atoms-search <query> — FTS over frontmatter + body
Tolerant scan: invalid frontmatter → stderr warn + continue (never abort).
[[rules/...]] wikilinks filtered at edge resolution per scope (rules
integration deferred to follow-up).
Tests: 9 unit + 6 integration smoke + 8 pre-existing = 23/23 green.
Zero regression. Single new dep: serde_yaml 0.9.
Stream C of substrate v1 parallel build.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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