diff --git a/_primitives/_rust/Cargo.lock b/_primitives/_rust/Cargo.lock
index 455e72c..439b685 100644
--- a/_primitives/_rust/Cargo.lock
+++ b/_primitives/_rust/Cargo.lock
@@ -1968,6 +1968,7 @@ dependencies = [
  "rusqlite",
  "serde",
  "serde_json",
+ "serde_yaml",
  "tempfile",
 ]
 
diff --git a/_primitives/_rust/kei-sage/Cargo.toml b/_primitives/_rust/kei-sage/Cargo.toml
index a9643cd..9bf1080 100644
--- a/_primitives/_rust/kei-sage/Cargo.toml
+++ b/_primitives/_rust/kei-sage/Cargo.toml
@@ -18,6 +18,7 @@ rusqlite = { version = "0.31", features = ["bundled"] }
 clap = { version = "4", features = ["derive"] }
 serde = { version = "1", features = ["derive"] }
 serde_json = "1"
+serde_yaml = "0.9"
 anyhow = "1"
 chrono = { version = "0.4", default-features = false, features = ["clock"] }
 
diff --git a/_primitives/_rust/kei-sage/src/atom_cli.rs b/_primitives/_rust/kei-sage/src/atom_cli.rs
new file mode 100644
index 0000000..0aee6be
--- /dev/null
+++ b/_primitives/_rust/kei-sage/src/atom_cli.rs
@@ -0,0 +1,73 @@
+//! CLI handlers for `atoms-*` subcommands — walks, indexes, queries atoms.
+//!
+//! Separate from `main.rs` to keep both files under Constructor Pattern
+//! 200-LOC limit. `main.rs` wires clap, this module implements the verbs.
+
+use crate::atom_index::index_atoms;
+use crate::atoms::{discover_atoms, AtomRecord};
+use crate::bfs::bfs;
+use crate::pagerank::pagerank;
+use crate::search::fts_search;
+use crate::store::Store;
+use anyhow::Result;
+use std::path::{Path, PathBuf};
+
+pub fn default_atoms_root() -> PathBuf {
+    let home = std::env::var("HOME").unwrap_or_else(|_| ".".into());
+    PathBuf::from(home).join(".claude/agents/_primitives/_rust")
+}
+
+pub fn cmd_atoms_discover(root: &Path) -> Result<()> {
+    let records = discover_atoms(root)?;
+    println!("full_id\tkind\tstability\tmd_path");
+    for r in &records {
+        println!(
+            "{}\t{}\t{}\t{}",
+            r.full_id,
+            r.kind.as_str(),
+            r.stability,
+            r.md_path.display()
+        );
+    }
+    eprintln!("discovered {} atom(s) under {}", records.len(), root.display());
+    Ok(())
+}
+
+pub fn cmd_atoms_rank(store: &Store, root: &Path, limit: usize) -> Result<()> {
+    ingest(store, root)?;
+    for (path, score) in pagerank(store)?.into_iter().take(limit) {
+        println!("{:.6}\t{}", score, path);
+    }
+    Ok(())
+}
+
+pub fn cmd_atoms_related(store: &Store, root: &Path, atom_id: &str, depth: i64) -> Result<()> {
+    ingest(store, root)?;
+    for r in bfs(store, atom_id, depth)? {
+        println!("{}\t{}\t(depth {})", r.edge_type, r.path, r.depth);
+    }
+    Ok(())
+}
+
+pub fn cmd_atoms_search(store: &Store, root: &Path, query: &str, limit: i64) -> Result<()> {
+    ingest(store, root)?;
+    for u in fts_search(store, query, limit)? {
+        if u.unit_type != "atom" {
+            continue;
+        }
+        println!("{}\t{}\t{}", u.id, u.category, u.vault_path);
+    }
+    Ok(())
+}
+
+fn ingest(store: &Store, root: &Path) -> Result<Vec<AtomRecord>> {
+    let records = discover_atoms(root)?;
+    let stats = index_atoms(store, &records)?;
+    eprintln!(
+        "indexed {} atom(s), {} wikilink edge(s) from {}",
+        stats.units_indexed,
+        stats.edges_indexed,
+        root.display()
+    );
+    Ok(records)
+}
diff --git a/_primitives/_rust/kei-sage/src/atom_index.rs b/_primitives/_rust/kei-sage/src/atom_index.rs
new file mode 100644
index 0000000..175c1da
--- /dev/null
+++ b/_primitives/_rust/kei-sage/src/atom_index.rs
@@ -0,0 +1,63 @@
+//! Persist discovered atoms into the kei-sage Store as Units + typed edges.
+//!
+//! Unit-type = `"atom"`; `vault_path` = atom full_id (e.g. `kei-task::create`).
+//! Edge-type = `"atom_related"` for wikilinks between atoms. Idempotent:
+//! re-ingesting the same corpus replaces existing rows by vault_path.
+
+use crate::atoms::{resolve_wikilinks, AtomRecord};
+use crate::edges::add_edge;
+use crate::store::Store;
+use crate::types::Unit;
+use anyhow::Result;
+
+pub struct IndexStats {
+    pub units_indexed: usize,
+    pub edges_indexed: usize,
+}
+
+pub fn index_atoms(store: &Store, records: &[AtomRecord]) -> Result<IndexStats> {
+    let units_indexed = index_units(store, records)?;
+    let edges_indexed = index_edges(store, records)?;
+    Ok(IndexStats { units_indexed, edges_indexed })
+}
+
+fn index_units(store: &Store, records: &[AtomRecord]) -> Result<usize> {
+    let mut n = 0;
+    for rec in records {
+        store.add_unit(&record_to_unit(rec))?;
+        n += 1;
+    }
+    Ok(n)
+}
+
+fn record_to_unit(rec: &AtomRecord) -> Unit {
+    Unit {
+        unit_type: "atom".into(),
+        title: rec.full_id.clone(),
+        content: build_content(rec),
+        evidence_grade: rec.stability.clone(),
+        source_path: rec.md_path.to_string_lossy().into(),
+        vault_path: rec.full_id.clone(),
+        category: rec.kind.as_str().into(),
+        ..Default::default()
+    }
+}
+
+fn build_content(rec: &AtomRecord) -> String {
+    let kw = rec.keywords.join(", ");
+    let mut s = String::with_capacity(rec.body.len() + kw.len() + 64);
+    s.push_str("[keywords] ");
+    s.push_str(&kw);
+    s.push_str("\n\n");
+    s.push_str(&rec.body);
+    s
+}
+
+fn index_edges(store: &Store, records: &[AtomRecord]) -> Result<usize> {
+    let mut n = 0;
+    for (src, dst) in resolve_wikilinks(records) {
+        add_edge(store, &src, &dst, "atom_related", 1.0)?;
+        n += 1;
+    }
+    Ok(n)
+}
diff --git a/_primitives/_rust/kei-sage/src/atom_parse.rs b/_primitives/_rust/kei-sage/src/atom_parse.rs
new file mode 100644
index 0000000..8e44e6c
--- /dev/null
+++ b/_primitives/_rust/kei-sage/src/atom_parse.rs
@@ -0,0 +1,121 @@
+//! Frontmatter splitting + wikilink extraction helpers for atom `.md` files.
+//!
+//! Pure functions, no I/O. See `atoms.rs` for the discovery walker.
+
+use anyhow::{anyhow, Result};
+
+/// Split a `.md` file into (frontmatter_yaml, body). Frontmatter must start
+/// with `---\n` and end with a line that is exactly `---`.
+pub fn split_frontmatter(text: &str) -> Result<(&str, &str)> {
+    let rest = text
+        .strip_prefix("---\n")
+        .or_else(|| text.strip_prefix("---\r\n"))
+        .ok_or_else(|| anyhow!("missing leading --- frontmatter delimiter"))?;
+    let end = find_closing_delim(rest)
+        .ok_or_else(|| anyhow!("missing closing --- frontmatter delimiter"))?;
+    let fm = &rest[..end.0];
+    let body_start = end.0 + end.1;
+    Ok((fm, rest.get(body_start..).unwrap_or("")))
+}
+
+fn find_closing_delim(s: &str) -> Option<(usize, usize)> {
+    let mut i = 0;
+    for line in s.split_inclusive('\n') {
+        let trimmed = line.trim_end_matches(&['\n', '\r'][..]);
+        if trimmed == "---" {
+            return Some((i, line.len()));
+        }
+        i += line.len();
+    }
+    None
+}
+
+/// Parse a single wikilink `[[target]]`. Returns `Some(target)` stripped of
+/// brackets and whitespace, `None` if the string isn't a wikilink shape.
+pub fn parse_wikilink(raw: &str) -> Option<String> {
+    let t = raw.trim();
+    let inner = t.strip_prefix("[[").and_then(|s| s.strip_suffix("]]"))?;
+    let inner = inner.trim();
+    if inner.is_empty() {
+        None
+    } else {
+        Some(inner.to_string())
+    }
+}
+
+/// Filter rule that decides whether a wikilink target is an atom reference.
+/// Atoms use `<crate>::<verb>`; we exclude `rules/*` and `rule*` targets.
+pub fn is_atom_target(target: &str) -> bool {
+    !target.starts_with("rules/") && !target.starts_with("rule ")
+}
+
+/// Split `<crate>::<verb>` atom id into components.
+pub fn split_atom_id(id: &str) -> Result<(String, String)> {
+    match id.split_once("::") {
+        Some((c, v)) if !c.is_empty() && !v.is_empty() => Ok((c.into(), v.into())),
+        _ => Err(anyhow!("atom id must be <crate>::<verb>, got {id}")),
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn split_basic() {
+        let src = "---\nfoo: bar\n---\nbody text\n";
+        let (fm, body) = split_frontmatter(src).unwrap();
+        assert_eq!(fm, "foo: bar\n");
+        assert_eq!(body, "body text\n");
+    }
+
+    #[test]
+    fn split_crlf() {
+        let src = "---\r\nfoo: bar\r\n---\r\nbody\r\n";
+        let (fm, _body) = split_frontmatter(src).unwrap();
+        assert!(fm.contains("foo: bar"));
+    }
+
+    #[test]
+    fn split_missing_start() {
+        assert!(split_frontmatter("no frontmatter\n").is_err());
+    }
+
+    #[test]
+    fn split_missing_end() {
+        assert!(split_frontmatter("---\nfoo: bar\nbody\n").is_err());
+    }
+
+    #[test]
+    fn wikilink_simple() {
+        assert_eq!(
+            parse_wikilink("[[kei-task::create]]"),
+            Some("kei-task::create".into())
+        );
+    }
+
+    #[test]
+    fn wikilink_none() {
+        assert_eq!(parse_wikilink("just text"), None);
+        assert_eq!(parse_wikilink("[[ ]]"), None);
+    }
+
+    #[test]
+    fn atom_target_filter() {
+        assert!(is_atom_target("kei-task::create"));
+        assert!(!is_atom_target("rules/RULE 0.12"));
+    }
+
+    #[test]
+    fn split_id_ok() {
+        let (c, v) = split_atom_id("kei-task::create").unwrap();
+        assert_eq!(c, "kei-task");
+        assert_eq!(v, "create");
+    }
+
+    #[test]
+    fn split_id_bad() {
+        assert!(split_atom_id("no-separator").is_err());
+        assert!(split_atom_id("::empty").is_err());
+    }
+}
diff --git a/_primitives/_rust/kei-sage/src/atoms.rs b/_primitives/_rust/kei-sage/src/atoms.rs
new file mode 100644
index 0000000..8273382
--- /dev/null
+++ b/_primitives/_rust/kei-sage/src/atoms.rs
@@ -0,0 +1,179 @@
+//! Substrate-atom discovery + frontmatter parsing + wikilink extraction.
+//!
+//! Walks `<root>/<crate>/atoms/*.md`, parses YAML frontmatter, returns
+//! `AtomRecord`. Tolerant: skips files with invalid frontmatter (logs to
+//! stderr, continues scan). See `docs/SUBSTRATE-SCHEMA.md` §Graph contract.
+
+use crate::atom_parse::{is_atom_target, parse_wikilink, split_atom_id, split_frontmatter};
+use anyhow::{anyhow, Context, Result};
+use serde::Deserialize;
+use std::fs;
+use std::path::{Path, PathBuf};
+use std::str::FromStr;
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub enum AtomKind {
+    Command,
+    Query,
+    Stream,
+    Transform,
+}
+
+impl FromStr for AtomKind {
+    type Err = anyhow::Error;
+    fn from_str(s: &str) -> Result<Self> {
+        match s.trim().to_ascii_lowercase().as_str() {
+            "command" => Ok(AtomKind::Command),
+            "query" => Ok(AtomKind::Query),
+            "stream" => Ok(AtomKind::Stream),
+            "transform" => Ok(AtomKind::Transform),
+            other => Err(anyhow!("unknown atom kind: {other}")),
+        }
+    }
+}
+
+impl AtomKind {
+    pub fn as_str(&self) -> &'static str {
+        match self {
+            AtomKind::Command => "command",
+            AtomKind::Query => "query",
+            AtomKind::Stream => "stream",
+            AtomKind::Transform => "transform",
+        }
+    }
+}
+
+#[derive(Debug, Clone)]
+pub struct AtomRecord {
+    pub full_id: String,
+    pub kind: AtomKind,
+    pub crate_name: String,
+    pub verb: String,
+    pub version: String,
+    pub md_path: PathBuf,
+    pub input_schema: Option<PathBuf>,
+    pub output_schema: Option<PathBuf>,
+    pub related: Vec<String>,
+    pub keywords: Vec<String>,
+    pub stability: String,
+    pub body: String,
+}
+
+#[derive(Debug, Deserialize)]
+struct SchemaRef {
+    schema: Option<String>,
+}
+
+#[derive(Debug, Deserialize)]
+struct Frontmatter {
+    atom: String,
+    kind: String,
+    #[serde(default)]
+    version: Option<String>,
+    #[serde(default)]
+    input: Option<SchemaRef>,
+    #[serde(default)]
+    output: Option<SchemaRef>,
+    #[serde(default)]
+    related: Vec<String>,
+    #[serde(default)]
+    keywords: Vec<String>,
+    #[serde(default)]
+    stability: Option<String>,
+}
+
+pub fn discover_atoms(root: &Path) -> Result<Vec<AtomRecord>> {
+    let mut out = Vec::new();
+    if !root.is_dir() {
+        return Ok(out);
+    }
+    for entry in fs::read_dir(root).with_context(|| format!("read_dir {}", root.display()))? {
+        let crate_dir = entry?.path();
+        if crate_dir.is_dir() {
+            collect_from_crate(&crate_dir, &mut out);
+        }
+    }
+    Ok(out)
+}
+
+fn collect_from_crate(crate_dir: &Path, out: &mut Vec<AtomRecord>) {
+    let atoms_dir = crate_dir.join("atoms");
+    if !atoms_dir.is_dir() {
+        return;
+    }
+    let crate_name = crate_dir
+        .file_name()
+        .and_then(|s| s.to_str())
+        .unwrap_or("")
+        .to_string();
+    let iter = match fs::read_dir(&atoms_dir) {
+        Ok(it) => it,
+        Err(e) => {
+            eprintln!("skip {}: {}", atoms_dir.display(), e);
+            return;
+        }
+    };
+    for entry in iter.flatten() {
+        let path = entry.path();
+        if !is_md_file(&path) {
+            continue;
+        }
+        match parse_atom_file(&path, &crate_name) {
+            Ok(rec) => out.push(rec),
+            Err(e) => eprintln!("skip {}: {}", path.display(), e),
+        }
+    }
+}
+
+fn is_md_file(path: &Path) -> bool {
+    path.is_file() && path.extension().and_then(|s| s.to_str()) == Some("md")
+}
+
+fn parse_atom_file(path: &Path, crate_name: &str) -> Result<AtomRecord> {
+    let text = fs::read_to_string(path)
+        .with_context(|| format!("read {}", path.display()))?;
+    let (fm_text, body) = split_frontmatter(&text)?;
+    let fm: Frontmatter =
+        serde_yaml::from_str(fm_text).with_context(|| "parse frontmatter YAML")?;
+    build_record(fm, body, path, crate_name)
+}
+
+fn build_record(fm: Frontmatter, body: &str, path: &Path, crate_name: &str) -> Result<AtomRecord> {
+    let kind = AtomKind::from_str(&fm.kind)?;
+    let (crate_from_id, verb) = split_atom_id(&fm.atom)?;
+    let md_dir = path.parent().unwrap_or(path).to_path_buf();
+    Ok(AtomRecord {
+        full_id: fm.atom.clone(),
+        kind,
+        crate_name: if crate_from_id.is_empty() {
+            crate_name.to_string()
+        } else {
+            crate_from_id
+        },
+        verb,
+        version: fm.version.unwrap_or_default(),
+        md_path: path.to_path_buf(),
+        input_schema: fm.input.and_then(|s| s.schema).map(|s| md_dir.join(&s)),
+        output_schema: fm.output.and_then(|s| s.schema).map(|s| md_dir.join(&s)),
+        related: fm.related,
+        keywords: fm.keywords,
+        stability: fm.stability.unwrap_or_else(|| "unknown".into()),
+        body: body.to_string(),
+    })
+}
+
+/// Extract `(source_atom_id, target)` edges from `related:` wikilinks.
+/// Non-atom targets (rules, notes) are filtered out here — scope: atoms only.
+pub fn resolve_wikilinks(records: &[AtomRecord]) -> Vec<(String, String)> {
+    let mut out = Vec::new();
+    for rec in records {
+        for w in &rec.related {
+            if let Some(target) = parse_wikilink(w) {
+                if is_atom_target(&target) {
+                    out.push((rec.full_id.clone(), target));
+                }
+            }
+        }
+    }
+    out
+}
diff --git a/_primitives/_rust/kei-sage/src/lib.rs b/_primitives/_rust/kei-sage/src/lib.rs
index 9980331..10f33d7 100644
--- a/_primitives/_rust/kei-sage/src/lib.rs
+++ b/_primitives/_rust/kei-sage/src/lib.rs
@@ -2,6 +2,10 @@
 //!
 //! Port of LBM internal/sage. Constructor Pattern: one concept per file.
 
+pub mod atom_cli;
+pub mod atom_index;
+pub mod atom_parse;
+pub mod atoms;
 pub mod bfs;
 pub mod edges;
 pub mod import;
diff --git a/_primitives/_rust/kei-sage/src/main.rs b/_primitives/_rust/kei-sage/src/main.rs
index 794c8d3..bee87b6 100644
--- a/_primitives/_rust/kei-sage/src/main.rs
+++ b/_primitives/_rust/kei-sage/src/main.rs
@@ -1,6 +1,9 @@
 //! kei-sage CLI — import / search / related / rank / add / edit.
 
 use clap::{Parser, Subcommand};
+use kei_sage::atom_cli::{
+    cmd_atoms_discover, cmd_atoms_related, cmd_atoms_search, cmd_atoms_rank, default_atoms_root,
+};
 use kei_sage::bfs::bfs;
 use kei_sage::edges::add_edge;
 use kei_sage::import::import_vault;
@@ -39,6 +42,23 @@ enum Cmd {
         #[arg(long)] grade: Option<String>,
     },
     Link { src: String, dst: String, #[arg(long, default_value = "related")] edge_type: String },
+    AtomsDiscover {
+        #[arg(long)] root: Option<PathBuf>,
+    },
+    AtomsRank {
+        #[arg(long)] root: Option<PathBuf>,
+        #[arg(long, default_value_t = 20)] limit: usize,
+    },
+    AtomsRelated {
+        atom_id: String,
+        #[arg(long)] root: Option<PathBuf>,
+        #[arg(long, default_value_t = 2)] depth: i64,
+    },
+    AtomsSearch {
+        query: String,
+        #[arg(long)] root: Option<PathBuf>,
+        #[arg(long, default_value_t = 20)] limit: i64,
+    },
 }
 
 fn db_path(cli_db: Option<PathBuf>) -> PathBuf {
@@ -65,6 +85,14 @@ fn dispatch(store: &Store, cmd: Cmd) -> anyhow::Result<()> {
         Cmd::Edit { id, title, content, grade } =>
             cmd_edit(store, id, title, content, grade),
         Cmd::Link { src, dst, edge_type } => cmd_link(store, &src, &dst, &edge_type),
+        Cmd::AtomsDiscover { root } =>
+            cmd_atoms_discover(&root.unwrap_or_else(default_atoms_root)),
+        Cmd::AtomsRank { root, limit } =>
+            cmd_atoms_rank(store, &root.unwrap_or_else(default_atoms_root), limit),
+        Cmd::AtomsRelated { atom_id, root, depth } =>
+            cmd_atoms_related(store, &root.unwrap_or_else(default_atoms_root), &atom_id, depth),
+        Cmd::AtomsSearch { query, root, limit } =>
+            cmd_atoms_search(store, &root.unwrap_or_else(default_atoms_root), &query, limit),
     }
 }
 
diff --git a/_primitives/_rust/kei-sage/tests/atoms_discover_smoke.rs b/_primitives/_rust/kei-sage/tests/atoms_discover_smoke.rs
new file mode 100644
index 0000000..a99d881
--- /dev/null
+++ b/_primitives/_rust/kei-sage/tests/atoms_discover_smoke.rs
@@ -0,0 +1,134 @@
+//! Integration smoke test for atom discovery + wikilink resolution.
+//!
+//! Creates a temp root with 2 fake crates, each with `atoms/<verb>.md`,
+//! asserts `discover_atoms` returns 2 records and frontmatter is parsed.
+
+use kei_sage::atom_index::index_atoms;
+use kei_sage::atoms::{discover_atoms, resolve_wikilinks, AtomKind};
+use kei_sage::Store;
+use std::fs;
+use tempfile::tempdir;
+
+const ATOM_A: &str = r#"---
+atom: kei-task::create
+kind: command
+version: "0.1.0"
+input:
+  schema: schemas/create-input.json
+output:
+  schema: schemas/create-output.json
+stability: stable
+keywords: [task, todo]
+related:
+  - "[[kei-task::add-dependency]]"
+  - "[[rules/RULE 0.12]]"
+---
+# kei-task::create
+
+Creates a task.
+"#;
+
+const ATOM_B: &str = r#"---
+atom: kei-task::add-dependency
+kind: command
+version: "0.1.0"
+stability: beta
+keywords: [task, dag]
+related: []
+---
+# kei-task::add-dependency
+
+Links two tasks.
+"#;
+
+const ATOM_BAD: &str = r#"not-yaml-frontmatter
+
+just a plain markdown file
+"#;
+
+fn write_atom(root: &std::path::Path, crate_name: &str, verb: &str, body: &str) {
+    let atoms_dir = root.join(crate_name).join("atoms");
+    fs::create_dir_all(&atoms_dir).unwrap();
+    fs::write(atoms_dir.join(format!("{verb}.md")), body).unwrap();
+}
+
+#[test]
+fn discover_returns_both_records() {
+    let tmp = tempdir().unwrap();
+    write_atom(tmp.path(), "kei-task", "create", ATOM_A);
+    write_atom(tmp.path(), "kei-task", "add-dependency", ATOM_B);
+
+    let recs = discover_atoms(tmp.path()).unwrap();
+    assert_eq!(recs.len(), 2, "expected 2 records, got {}", recs.len());
+
+    let ids: Vec<&str> = recs.iter().map(|r| r.full_id.as_str()).collect();
+    assert!(ids.contains(&"kei-task::create"));
+    assert!(ids.contains(&"kei-task::add-dependency"));
+}
+
+#[test]
+fn frontmatter_fields_parsed() {
+    let tmp = tempdir().unwrap();
+    write_atom(tmp.path(), "kei-task", "create", ATOM_A);
+
+    let recs = discover_atoms(tmp.path()).unwrap();
+    let rec = recs.iter().find(|r| r.full_id == "kei-task::create").unwrap();
+
+    assert_eq!(rec.kind, AtomKind::Command);
+    assert_eq!(rec.crate_name, "kei-task");
+    assert_eq!(rec.verb, "create");
+    assert_eq!(rec.version, "0.1.0");
+    assert_eq!(rec.stability, "stable");
+    assert!(rec.keywords.contains(&"task".to_string()));
+    assert!(rec.input_schema.is_some());
+    assert!(rec.output_schema.is_some());
+    assert!(rec.body.contains("Creates a task"));
+}
+
+#[test]
+fn invalid_frontmatter_is_skipped_not_fatal() {
+    let tmp = tempdir().unwrap();
+    write_atom(tmp.path(), "kei-task", "create", ATOM_A);
+    write_atom(tmp.path(), "kei-task", "broken", ATOM_BAD);
+
+    let recs = discover_atoms(tmp.path()).unwrap();
+    assert_eq!(recs.len(), 1);
+    assert_eq!(recs[0].full_id, "kei-task::create");
+}
+
+#[test]
+fn wikilinks_filter_rule_targets() {
+    let tmp = tempdir().unwrap();
+    write_atom(tmp.path(), "kei-task", "create", ATOM_A);
+    write_atom(tmp.path(), "kei-task", "add-dependency", ATOM_B);
+
+    let recs = discover_atoms(tmp.path()).unwrap();
+    let edges = resolve_wikilinks(&recs);
+
+    // Only atom-to-atom edges remain; `[[rules/RULE 0.12]]` filtered.
+    assert_eq!(edges.len(), 1);
+    assert_eq!(edges[0].0, "kei-task::create");
+    assert_eq!(edges[0].1, "kei-task::add-dependency");
+}
+
+#[test]
+fn empty_root_returns_empty() {
+    let tmp = tempdir().unwrap();
+    let recs = discover_atoms(tmp.path()).unwrap();
+    assert!(recs.is_empty());
+}
+
+#[test]
+fn index_atoms_persists_units_and_edges() {
+    let tmp = tempdir().unwrap();
+    write_atom(tmp.path(), "kei-task", "create", ATOM_A);
+    write_atom(tmp.path(), "kei-task", "add-dependency", ATOM_B);
+
+    let recs = discover_atoms(tmp.path()).unwrap();
+    let store = Store::open_memory().unwrap();
+    let stats = index_atoms(&store, &recs).unwrap();
+
+    assert_eq!(stats.units_indexed, 2);
+    assert_eq!(stats.edges_indexed, 1);
+    assert_eq!(store.count_units().unwrap(), 2);
+}