fix: context engine cleanup — resolve N+1 queries, consolidate resolution

- Add find_file_by_basename store method (SQL instead of get_all_files)
- Add edge_counts_for_files batch method (single query instead of N+1)
- Consolidate file resolution: context_who, context_project, graph CLI
  all delegate to resolve_file/find_file_by_basename
- Fix ProjectContext.total_chars to include children and tasks
- Rename char_count to byte_count for accuracy

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: devwhodevs

src/context.rs

@@ -26,7 +26,7 @@ pub struct NoteContent {
     pub incoming_links: Vec<String>,
     pub mentions_people: Vec<String>,
     pub mentioned_by: Vec<String>,
-    pub char_count: usize,
+    pub byte_count: usize,
 }
 
 #[derive(Debug, Serialize)]
@@ -110,18 +110,8 @@ fn resolve_file(
         return Ok(Some(f));
     }
 
-    // Basename fallback: append .md if needed, then case-insensitive suffix match
-    let target = if file_or_docid.ends_with(".md") {
-        file_or_docid.to_string()
-    } else {
-        format!("{}.md", file_or_docid)
-    };
-    let target_lower = target.to_lowercase();
-    let all = params.store.get_all_files()?;
-    Ok(all.into_iter().find(|f| {
-        let p = f.path.to_lowercase();
-        p == target_lower || p.ends_with(&format!("/{}", target_lower))
-    }))
+    // Basename fallback via SQL
+    params.store.find_file_by_basename(file_or_docid)
 }
 
 /// Split content into (frontmatter YAML, body) parts.
@@ -190,7 +180,7 @@ pub fn context_read(params: &ContextParams, file_or_docid: &str) -> Result<NoteC
         .filter_map(|(fid, _)| params.store.get_file_path_by_id(*fid).ok().flatten())
         .collect();
 
-    let char_count = content.len();
+    let byte_count = content.len();
     Ok(NoteContent {
         path: record.path,
         docid: record.docid,
@@ -202,7 +192,7 @@ pub fn context_read(params: &ContextParams, file_or_docid: &str) -> Result<NoteC
         incoming_links,
         mentions_people,
         mentioned_by,
-        char_count,
+        byte_count,
     })
 }
 
@@ -214,9 +204,14 @@ pub fn context_list(
     limit: usize,
 ) -> Result<Vec<NoteListItem>> {
     let files = params.store.list_files(folder, tags, limit)?;
+    let file_ids: Vec<i64> = files.iter().map(|f| f.id).collect();
+    let edge_counts = params
+        .store
+        .edge_counts_for_files(&file_ids)
+        .unwrap_or_default();
     let mut items = Vec::new();
     for f in files {
-        let edge_count = params.store.edge_count_for_file(f.id).unwrap_or(0);
+        let edge_count = edge_counts.get(&f.id).copied().unwrap_or(0);
         items.push(NoteListItem {
             path: f.path,
             docid: f.docid,
@@ -270,15 +265,7 @@ pub fn vault_map(params: &ContextParams) -> Result<VaultMap> {
 
 /// Build a person context bundle: note content, mentions, wikilink connections.
 pub fn context_who(params: &ContextParams, name: &str) -> Result<PersonContext> {
-    let name_md = format!("{}.md", name);
-    let name_lower = name_md.to_lowercase();
-    let all_files = params.store.get_all_files()?;
-    let person_file = all_files.iter().find(|f| {
-        let basename = f.path.rsplit('/').next().unwrap_or(&f.path).to_lowercase();
-        basename == name_lower
-    });
-
-    let (note, person_id) = if let Some(pf) = person_file {
+    let (note, person_id) = if let Some(pf) = resolve_file(params, name)? {
         let n = context_read(params, &pf.path)?;
         (Some(n), Some(pf.id))
     } else {
@@ -323,7 +310,7 @@ pub fn context_who(params: &ContextParams, name: &str) -> Result<PersonContext>
         }
     }
 
-    let total_chars = note.as_ref().map(|n| n.char_count).unwrap_or(0)
+    let total_chars = note.as_ref().map(|n| n.byte_count).unwrap_or(0)
         + mentioned_in.iter().map(|m| m.snippet.len()).sum::<usize>();
 
     Ok(PersonContext {
@@ -364,38 +351,23 @@ fn get_mention_snippet(params: &ContextParams, file_id: i64, name: &str) -> Stri
 
 /// Build a project context bundle: note, child notes, tasks, team, recent mentions.
 pub fn context_project(params: &ContextParams, name: &str) -> Result<ProjectContext> {
-    let name_md = format!("{}.md", name);
-    let name_lower = name_md.to_lowercase();
-    let all_files = params.store.get_all_files()?;
-    let project_file = all_files.iter().find(|f| {
-        let basename = f.path.rsplit('/').next().unwrap_or(&f.path).to_lowercase();
-        basename == name_lower
-    });
-
-    let (note, project_id, project_folder) = if let Some(pf) = project_file {
-        let n = context_read(params, &pf.path)?;
+    let (note, project_id, project_folder) = if let Some(pf) = resolve_file(params, name)? {
         let folder = pf.path.rsplit_once('/').map(|(f, _)| f.to_string());
+        let n = context_read(params, &pf.path)?;
         (Some(n), Some(pf.id), folder)
     } else {
         (None, None, None)
     };
 
     let mut child_ids = HashSet::new();
-    let mut child_notes = Vec::new();
+    let mut child_records: Vec<crate::store::FileRecord> = Vec::new();
 
     // Files in same folder
     if let Some(folder) = &project_folder {
         let folder_files = params.store.list_files(Some(folder), &[], 50)?;
         for f in folder_files {
             if Some(f.id) != project_id && child_ids.insert(f.id) {
-                let ec = params.store.edge_count_for_file(f.id).unwrap_or(0);
-                child_notes.push(NoteListItem {
-                    path: f.path,
-                    docid: f.docid,
-                    tags: f.tags,
-                    indexed_at: f.indexed_at,
-                    edge_count: ec,
-                });
+                child_records.push(f);
             }
         }
     }
@@ -407,18 +379,31 @@ pub fn context_project(params: &ContextParams, name: &str) -> Result<ProjectCont
             if child_ids.insert(*fid)
                 && let Some(f) = params.store.get_file_by_id(*fid).ok().flatten()
             {
-                let ec = params.store.edge_count_for_file(*fid).unwrap_or(0);
-                child_notes.push(NoteListItem {
-                    path: f.path,
-                    docid: f.docid,
-                    tags: f.tags,
-                    indexed_at: f.indexed_at,
-                    edge_count: ec,
-                });
+                child_records.push(f);
             }
         }
     }
 
+    // Batch edge counts for all children
+    let child_file_ids: Vec<i64> = child_records.iter().map(|f| f.id).collect();
+    let edge_counts = params
+        .store
+        .edge_counts_for_files(&child_file_ids)
+        .unwrap_or_default();
+    let child_notes: Vec<NoteListItem> = child_records
+        .into_iter()
+        .map(|f| {
+            let ec = edge_counts.get(&f.id).copied().unwrap_or(0);
+            NoteListItem {
+                path: f.path,
+                docid: f.docid,
+                tags: f.tags,
+                indexed_at: f.indexed_at,
+                edge_count: ec,
+            }
+        })
+        .collect();
+
     // Active tasks
     let mut active_tasks = Vec::new();
     let scan_tasks = |path: &str, tasks: &mut Vec<TaskItem>| {
@@ -483,7 +468,15 @@ pub fn context_project(params: &ContextParams, name: &str) -> Result<ProjectCont
         }
     }
 
-    let total_chars = note.as_ref().map(|n| n.char_count).unwrap_or(0);
+    let total_chars = note.as_ref().map(|n| n.byte_count).unwrap_or(0)
+        + child_notes
+            .iter()
+            .filter_map(|c| {
+                let full = params.vault_path.join(&c.path);
+                std::fs::metadata(&full).ok().map(|m| m.len() as usize)
+            })
+            .sum::<usize>()
+        + active_tasks.iter().map(|t| t.text.len()).sum::<usize>();
 
     Ok(ProjectContext {
         name: name.to_string(),
@@ -700,7 +693,7 @@ mod tests {
         assert!(note.tags.contains(&"rust".to_string()));
         assert_eq!(note.outgoing_links.len(), 1);
         assert_eq!(note.incoming_links.len(), 1);
-        assert!(note.char_count > 0);
+        assert!(note.byte_count > 0);
     }
 
     #[test]

src/main.rs

@@ -396,19 +396,7 @@ fn main() -> Result<()> {
                     } else if let Some(f) = store.get_file(&file)? {
                         Some(f)
                     } else {
-                        // Basename match (case-insensitive)
-                        let target = if file.ends_with(".md") {
-                            file.clone()
-                        } else {
-                            format!("{}.md", file)
-                        };
-                        let all = store.get_all_files()?;
-                        let target_lower = target.to_lowercase();
-                        all.into_iter().find(|f| {
-                            let path_lower = f.path.to_lowercase();
-                            path_lower == target_lower
-                                || path_lower.ends_with(&format!("/{}", target_lower))
-                        })
+                        store.find_file_by_basename(&file)?
                     };
 
                     let record = match record {
@@ -543,7 +531,7 @@ fn main() -> Result<()> {
                         println!("Tags: {}", note.tags.join(", "));
                         println!("Outgoing links: {}", note.outgoing_links.len());
                         println!("Incoming links: {}", note.incoming_links.len());
-                        println!("Chars: {}\n", note.char_count);
+                        println!("Bytes: {}\n", note.byte_count);
                         println!("{}", note.body);
                     }
                 }

src/store.rs

@@ -903,6 +903,75 @@ impl Store {
         )?;
         Ok(count as usize)
     }
+
+    /// Get edge counts for multiple files in a single query.
+    pub fn edge_counts_for_files(
+        &self,
+        file_ids: &[i64],
+    ) -> Result<std::collections::HashMap<i64, usize>> {
+        use std::collections::HashMap;
+        if file_ids.is_empty() {
+            return Ok(HashMap::new());
+        }
+        let placeholders: Vec<String> = file_ids.iter().map(|_| "?".to_string()).collect();
+        let ph = placeholders.join(",");
+        let sql = format!(
+            "SELECT fid, COUNT(*) FROM (
+                SELECT from_file AS fid FROM edges WHERE from_file IN ({ph})
+                UNION ALL
+                SELECT to_file AS fid FROM edges WHERE to_file IN ({ph})
+            ) GROUP BY fid"
+        );
+        let mut stmt = self.conn.prepare(&sql)?;
+        let params: Vec<Box<dyn rusqlite::types::ToSql>> = file_ids
+            .iter()
+            .chain(file_ids.iter())
+            .map(|id| Box::new(*id) as Box<dyn rusqlite::types::ToSql>)
+            .collect();
+        let rows = stmt.query_map(rusqlite::params_from_iter(params.iter()), |row| {
+            Ok((row.get::<_, i64>(0)?, row.get::<_, i64>(1)? as usize))
+        })?;
+        let mut map = HashMap::new();
+        for row in rows {
+            let (id, count) = row?;
+            map.insert(id, count);
+        }
+        Ok(map)
+    }
+
+    /// Find a file by case-insensitive basename match. Returns first match (shortest path).
+    pub fn find_file_by_basename(&self, basename: &str) -> Result<Option<FileRecord>> {
+        let target = if basename.ends_with(".md") {
+            basename.to_string()
+        } else {
+            format!("{}.md", basename)
+        };
+        // Try exact path first
+        if let Some(f) = self.get_file(&target)? {
+            return Ok(Some(f));
+        }
+        // Basename match via SQL
+        let mut stmt = self.conn.prepare(
+            "SELECT id, path, content_hash, mtime, tags, indexed_at, docid FROM files
+             WHERE lower(path) LIKE '%/' || lower(?1) OR lower(path) = lower(?1)
+             ORDER BY length(path) ASC LIMIT 1",
+        )?;
+        let mut rows = stmt.query_map(params![target], |row| {
+            Ok(FileRecord {
+                id: row.get(0)?,
+                path: row.get(1)?,
+                content_hash: row.get(2)?,
+                mtime: row.get(3)?,
+                tags: parse_tags(&row.get::<_, String>(4)?),
+                indexed_at: row.get(5)?,
+                docid: row.get(6)?,
+            })
+        })?;
+        match rows.next() {
+            Some(r) => Ok(Some(r?)),
+            None => Ok(None),
+        }
+    }
 }
 
 fn parse_tags(json: &str) -> Vec<String> {
@@ -1527,4 +1596,43 @@ mod tests {
         assert_eq!(store.edge_count_for_file(f1).unwrap(), 2);
         assert_eq!(store.edge_count_for_file(f2).unwrap(), 2);
     }
+
+    #[test]
+    fn test_find_file_by_basename() {
+        let store = Store::open_memory().unwrap();
+        store
+            .insert_file("01-Projects/Work/note.md", "h1", 100, &[], "aaa111")
+            .unwrap();
+        store
+            .insert_file("root.md", "h2", 100, &[], "bbb222")
+            .unwrap();
+
+        let found = store.find_file_by_basename("note").unwrap();
+        assert!(found.is_some());
+        assert_eq!(found.unwrap().path, "01-Projects/Work/note.md");
+
+        let found = store.find_file_by_basename("note.md").unwrap();
+        assert!(found.is_some());
+
+        let found = store.find_file_by_basename("nonexistent").unwrap();
+        assert!(found.is_none());
+    }
+
+    #[test]
+    fn test_edge_counts_for_files() {
+        let store = Store::open_memory().unwrap();
+        let f1 = store.insert_file("a.md", "h1", 100, &[], "a1").unwrap();
+        let f2 = store.insert_file("b.md", "h2", 100, &[], "b2").unwrap();
+        let f3 = store.insert_file("c.md", "h3", 100, &[], "c3").unwrap();
+        store.insert_edge(f1, f2, "wikilink").unwrap();
+        store.insert_edge(f2, f1, "wikilink").unwrap();
+        store.insert_edge(f1, f3, "wikilink").unwrap();
+        let counts = store.edge_counts_for_files(&[f1, f2, f3]).unwrap();
+        assert_eq!(*counts.get(&f1).unwrap(), 3);
+        assert_eq!(*counts.get(&f2).unwrap(), 2);
+        assert_eq!(*counts.get(&f3).unwrap(), 1);
+        // Empty input returns empty map
+        let empty = store.edge_counts_for_files(&[]).unwrap();
+        assert!(empty.is_empty());
+    }
 }