fix(dogfood): auto-purge stored docs for filesystem-deleted files

Files deleted from disk (rm a.md) were leaving stale documents + chunks +
embeddings in the store, surfacing as ghost citations in search/ask.
Existing purge_orphan_at_workspace_path only handled content-changed
stale (WHERE workspace_path=? AND asset_id != ?) — file deletion has no
new asset_id.

Fix: post-walker-scan sweep. Compute (stored_paths - scanned_paths),
for each candidate check filesystem existence — only purge when the
file is TRULY missing. Scope-narrowing case (file on disk but outside
include glob) is explicitly NOT purged to protect users from accidental
data loss via config edits.

Adds:
- DocumentStore::all_workspace_paths trait method + SqliteStore impl
- purge_deleted_workspace_path in store-sqlite (returns chunk_ids for
  vector delete; deletes doc CASCADE + asset row + copied storage file)
- sweep_deleted_files in kebab-app::ingest path; called once per ingest
  before the per-asset loop
- IngestReport.purged_deleted_files counter (additive, serde default)
- CLI ingest summary mentions purge count when > 0
- 2 integration tests: file_deletion_auto_purge + include_scope_narrowing_does_NOT_purge

dogfood discovery (PR #142 1B + multi-root: kebab-docs + httpx + zod
+ lodash). Per user decision: only filesystem deletion auto-purges;
scope narrowing requires explicit kebab reset.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

crates/kebab-app/src/lib.rs

@@ -375,6 +375,28 @@ pub fn ingest_with_config_opts(
         .map(|d| d.doc_id.0)
         .collect();
 
+    // Dogfood: post-walker sweep to remove stored docs whose source
+    // file has been deleted from the filesystem. Must run BEFORE the
+    // per-asset loop so the loop's New/Updated labelling is based on
+    // the post-purge store state (the purged doc_ids won't be in
+    // `existing_doc_ids` above — they were already removed, OR the
+    // sweep here removes them before we start counting).
+    //
+    // Critical design invariant: only purge when the file is TRULY
+    // absent from disk. A file that is still on disk but outside the
+    // current walker scope (config narrowing / include-glob change) is
+    // NOT purged — we leave it in place to protect against accidental
+    // data loss via config edits.
+    let scanned_paths: std::collections::HashSet<kebab_core::WorkspacePath> = assets
+        .iter()
+        .map(|a| a.workspace_path.clone())
+        .collect();
+    let purged_deleted_files = sweep_deleted_files(
+        &app,
+        &scanned_paths,
+        vector_store.as_ref().map(|v| v.as_ref()),
+    )?;
+
     let started_at = time::OffsetDateTime::now_utc();
 
     let mut items: Vec<kebab_core::IngestItem> = Vec::new();
@@ -647,11 +669,11 @@ pub fn ingest_with_config_opts(
     crate::ingest_progress::emit(progress, terminal_event);
 
     // p9-fb-19: bump the persistent corpus_revision counter when a
-    // commit landed (any new / updated). This invalidates every
+    // commit landed (any new / updated / purged). This invalidates every
     // entry in any in-process LRU search cache (in this process or
     // a sibling) on the next lookup. No-op when nothing changed
     // (skipped-only run) — the cache stays valid.
-    if new_count > 0 || updated_count > 0 {
+    if new_count > 0 || updated_count > 0 || purged_deleted_files > 0 {
         match app.sqlite.bump_corpus_revision() {
             Ok(rev) => tracing::debug!(
                 target: "kebab-app",
@@ -682,6 +704,7 @@ pub fn ingest_with_config_opts(
         skipped_generated: fs_skips.skipped_generated,
         skipped_size_exceeded: fs_skips.skipped_size_exceeded,
         skip_examples: fs_skips.skip_examples,
+        purged_deleted_files,
         items: if summary_only { None } else { Some(items) },
     })
 }
@@ -1453,6 +1476,112 @@ fn purge_vector_orphans_for_workspace_path(
     Ok(())
 }
 
+/// Dogfood: post-walker sweep that purges stored documents whose source
+/// file has been physically deleted from the filesystem.
+///
+/// Algorithm:
+/// 1. Query `documents` for every `workspace_path` currently stored.
+/// 2. Compute `orphan_candidates = stored_paths - scanned_paths`.
+/// 3. For each candidate: resolve to an absolute path and call
+///    `fs::exists()`. If the file still exists on disk it was merely
+///    out-of-scope this run (config narrowing / include-glob change) —
+///    leave it alone.  Only files that are truly absent trigger a purge.
+/// 4. For absent files: call `purge_deleted_workspace_path` (SQLite
+///    cascade delete + optional copied-asset file removal) and, if a
+///    vector store is present, delete the associated vectors.
+///
+/// Returns the number of documents purged.
+///
+/// Non-fatal design: individual purge failures are logged and counted
+/// as errors on the per-file level but do NOT abort the sweep — a
+/// partial failure is preferable to blocking the rest of ingest. The
+/// return value only counts successful purges.
+fn sweep_deleted_files(
+    app: &App,
+    scanned_paths: &std::collections::HashSet<kebab_core::WorkspacePath>,
+    vector_store: Option<&kebab_store_vector::LanceVectorStore>,
+) -> anyhow::Result<u32> {
+    use kebab_core::DocumentStore as _;
+
+    let stored_paths = app
+        .sqlite
+        .all_workspace_paths()
+        .context("sweep_deleted_files: all_workspace_paths")?;
+
+    if stored_paths.is_empty() {
+        return Ok(0);
+    }
+
+    let workspace_root = app.config.resolve_workspace_root();
+    let mut purged: u32 = 0;
+
+    for stored_path in stored_paths {
+        if scanned_paths.contains(&stored_path) {
+            continue; // still in scope — skip
+        }
+
+        // Resolve to an absolute path and check existence on disk.
+        // Files whose path cannot be joined (theoretically impossible
+        // for non-empty workspace_path strings, but defense-in-depth)
+        // are treated as "still present" to avoid accidental deletion.
+        let abs = workspace_root.join(&stored_path.0);
+        if abs.exists() {
+            // File is on disk but not in this scan's scope (config
+            // narrowing). DO NOT purge — critical design constraint.
+            tracing::debug!(
+                target: "kebab-app",
+                path = %stored_path.0,
+                "sweep_deleted_files: file on disk but out of scope — leaving in store"
+            );
+            continue;
+        }
+
+        // File is truly absent → purge.
+        let chunk_ids = match kebab_store_sqlite::purge_deleted_workspace_path(
+            &app.sqlite,
+            &stored_path,
+        ) {
+            Ok(ids) => ids,
+            Err(e) => {
+                tracing::warn!(
+                    target: "kebab-app",
+                    path = %stored_path.0,
+                    error = %e,
+                    "sweep_deleted_files: purge failed; skipping this path"
+                );
+                continue;
+            }
+        };
+
+        // Purge associated vectors (best-effort; partial failure
+        // acceptable — orphan vectors get cleaned by `kebab reset
+        // --vector-only` if they accumulate).
+        if let Some(vec) = vector_store {
+            if !chunk_ids.is_empty() {
+                use kebab_core::VectorStore as _;
+                if let Err(e) = vec.delete_by_chunk_ids(&chunk_ids) {
+                    tracing::warn!(
+                        target: "kebab-app",
+                        path = %stored_path.0,
+                        count = chunk_ids.len(),
+                        error = %e,
+                        "sweep_deleted_files: vector delete failed; SQLite side already cleaned"
+                    );
+                }
+            }
+        }
+
+        tracing::info!(
+            target: "kebab-app",
+            path = %stored_path.0,
+            "sweep_deleted_files: purged document for deleted file"
+        );
+        purged = purged.saturating_add(1);
+    }
+
+    Ok(purged)
+}
+
 /// P7-3: process one `MediaType::Pdf` asset end-to-end.
 ///
 /// - Reads bytes from disk.

crates/kebab-app/tests/file_deletion_auto_purge.rs

@@ -0,0 +1,178 @@
+//! Dogfood: auto-purge stored docs for filesystem-deleted files.
+//!
+//! Two tests:
+//!
+//! 1. `file_deletion_auto_purge` — ingest 2 files, delete one, re-ingest.
+//!    The re-ingest must report `purged_deleted_files = 1`, the deleted
+//!    file must no longer appear in `list_docs`, and lexical search for
+//!    its unique content must return no hits.
+//!
+//! 2. `include_scope_narrowing_does_not_purge` — ingest 2 files under a
+//!    wide glob, narrow the walker scope to only one file, re-ingest.
+//!    The narrowed ingest must NOT purge the out-of-scope file because
+//!    the file is still on disk (just excluded from this run). Protects
+//!    users against accidental data loss via config edits.
+
+mod common;
+
+use common::TestEnv;
+use kebab_app::ingest_with_config_opts;
+use kebab_app::IngestOpts;
+use kebab_core::{DocFilter, DocumentStore, SearchMode, SearchQuery, SourceScope};
+
+/// Helper: open the store via `TestEnv` and run `list_documents`.
+fn list_doc_paths(env: &TestEnv) -> Vec<String> {
+    use kebab_store_sqlite::SqliteStore;
+    let store = SqliteStore::open(&env.config).unwrap();
+    store.run_migrations().unwrap();
+    store
+        .list_documents(&DocFilter::default())
+        .unwrap()
+        .into_iter()
+        .map(|d| d.doc_path.0)
+        .collect()
+}
+
+#[test]
+fn file_deletion_auto_purge() {
+    let env = TestEnv::lexical_only();
+
+    // Write two .rs files into the workspace.
+    let a_path = env.workspace_root.join("a.rs");
+    let b_path = env.workspace_root.join("b.rs");
+    std::fs::write(&a_path, "// file a\nfn alpha() {}\n").unwrap();
+    std::fs::write(&b_path, "// file b\nfn bravo() {}\n").unwrap();
+
+    // First ingest — both must be New.
+    let first = ingest_with_config_opts(
+        env.config.clone(),
+        env.scope(),
+        false,
+        IngestOpts::default(),
+    )
+    .expect("first ingest must succeed");
+    // Only count the .rs files we added (there may be fixture files too).
+    let first_new = first.new;
+    assert!(first_new >= 2, "expected at least 2 new docs: {first:?}");
+    assert_eq!(
+        first.purged_deleted_files, 0,
+        "no purges on first ingest: {first:?}"
+    );
+    assert_eq!(first.errors, 0, "no errors on first ingest: {first:?}");
+
+    // Delete one file from the filesystem.
+    std::fs::remove_file(&b_path).expect("remove b.rs");
+
+    // Second ingest — scanned count drops by 1; b.rs should be purged.
+    let second = ingest_with_config_opts(
+        env.config.clone(),
+        env.scope(),
+        false,
+        IngestOpts::default(),
+    )
+    .expect("second ingest must succeed");
+
+    assert_eq!(
+        second.purged_deleted_files, 1,
+        "exactly 1 file should be purged: {second:?}"
+    );
+    assert_eq!(second.new, 0, "no new docs after deletion: {second:?}");
+    assert_eq!(second.updated, 0, "no updated docs: {second:?}");
+    assert_eq!(second.errors, 0, "no errors: {second:?}");
+
+    // b.rs must no longer appear in list_docs.
+    let doc_paths = list_doc_paths(&env);
+    let b_ws_path = "b.rs";
+    assert!(
+        !doc_paths.iter().any(|p| p == b_ws_path),
+        "b.rs must be gone from list_docs; got: {doc_paths:?}"
+    );
+    // a.rs must still be present.
+    let a_ws_path = "a.rs";
+    assert!(
+        doc_paths.iter().any(|p| p == a_ws_path),
+        "a.rs must still be in list_docs; got: {doc_paths:?}"
+    );
+
+    // Lexical search for b.rs's unique content returns no hits.
+    let app = env.app();
+    let query = SearchQuery {
+        text: "bravo".to_string(),
+        mode: SearchMode::Lexical,
+        k: 10,
+        filters: kebab_core::SearchFilters::default(),
+    };
+    let hits = app.search(query).expect("search must not error");
+    assert!(
+        hits.is_empty(),
+        "search for deleted file's content must return no hits; got: {hits:?}"
+    );
+}
+
+#[test]
+fn include_scope_narrowing_does_not_purge() {
+    let env = TestEnv::lexical_only();
+
+    // Write two .rs files.
+    let a_path = env.workspace_root.join("a_narrow.rs");
+    let b_path = env.workspace_root.join("b_narrow.rs");
+    std::fs::write(&a_path, "// narrow a\nfn alpha_narrow() {}\n").unwrap();
+    std::fs::write(&b_path, "// narrow b\nfn bravo_narrow() {}\n").unwrap();
+
+    // Wide scope: first ingest — both must be New.
+    let wide_scope = SourceScope {
+        root: env.workspace_root.clone(),
+        include: vec!["**/*.rs".to_string()],
+        exclude: env.config.workspace.exclude.clone(),
+    };
+    let first = ingest_with_config_opts(
+        env.config.clone(),
+        wide_scope,
+        false,
+        IngestOpts::default(),
+    )
+    .expect("first ingest (wide) must succeed");
+    assert!(
+        first.new >= 2,
+        "expected at least 2 new docs: {first:?}"
+    );
+    assert_eq!(
+        first.purged_deleted_files, 0,
+        "no purges on first ingest: {first:?}"
+    );
+
+    // Narrow scope: only a_narrow.rs in include — b_narrow.rs is still
+    // on disk but excluded from the walker scope.
+    let narrow_scope = SourceScope {
+        root: env.workspace_root.clone(),
+        include: vec!["a_narrow.rs".to_string()],
+        exclude: env.config.workspace.exclude.clone(),
+    };
+    let second = ingest_with_config_opts(
+        env.config.clone(),
+        narrow_scope,
+        false,
+        IngestOpts::default(),
+    )
+    .expect("second ingest (narrow) must succeed");
+
+    // CRITICAL: b_narrow.rs is still on disk — must NOT be purged.
+    assert_eq!(
+        second.purged_deleted_files, 0,
+        "scope-narrowing must NOT purge on-disk files; got: {second:?}"
+    );
+    assert_eq!(second.errors, 0, "no errors: {second:?}");
+
+    // b_narrow.rs must still exist in the store.
+    let doc_paths = list_doc_paths(&env);
+    let b_ws_path = "b_narrow.rs";
+    assert!(
+        doc_paths.iter().any(|p| p == b_ws_path),
+        "b_narrow.rs must still be in list_docs after scope narrowing; got: {doc_paths:?}"
+    );
+    // And the file must still be on disk.
+    assert!(
+        b_path.exists(),
+        "b_narrow.rs must still be on disk (we didn't delete it)"
+    );
+}

crates/kebab-cli/src/main.rs

@@ -595,14 +595,20 @@ fn run(cli: &Cli) -> anyhow::Result<()> {
                 println!("{}", serde_json::to_string(&wire::wire_ingest(&report))?);
             } else {
                 let skipped_breakdown = kebab_app::render_skipped_breakdown(&report.skipped_by_extension);
+                let purged_suffix = if report.purged_deleted_files > 0 {
+                    format!("  purged {}", report.purged_deleted_files)
+                } else {
+                    String::new()
+                };
                 println!(
-                    "scanned {}  new {}  updated {}  skipped {}{}  errors {}  ({} ms)",
+                    "scanned {}  new {}  updated {}  skipped {}{}  errors {}{}  ({} ms)",
                     report.scanned,
                     report.new,
                     report.updated,
                     report.skipped,
                     skipped_breakdown,
                     report.errors,
+                    purged_suffix,
                     report.duration_ms
                 );
             }

crates/kebab-cli/src/wire.rs

@@ -260,6 +260,7 @@ mod tests {
             skipped_generated: 0,
             skipped_size_exceeded: 0,
             skip_examples: SkipExamples::default(),
+            purged_deleted_files: 0,
             items: None,
         };
         let v = wire_ingest(&r);

crates/kebab-core/src/ingest.rs

@@ -47,6 +47,12 @@ pub struct IngestReport {
     /// p10-1A-1: sample file paths per skip category (≤ 5 each).
     #[serde(default)]
     pub skip_examples: SkipExamples,
+    /// Dogfood: docs whose on-disk file was deleted since the last ingest
+    /// and were therefore removed from the store. Additive field — older
+    /// wire consumers that pre-date this field read it as 0 via
+    /// `#[serde(default)]`.
+    #[serde(default)]
+    pub purged_deleted_files: u32,
     /// `None` ↔ wire `items: null` (`--summary-only`).
     pub items: Option<Vec<IngestItem>>,
 }
@@ -136,6 +142,7 @@ mod tests {
                 builtin_blacklist: vec!["node_modules/x.js".into()],
                 gitignore: vec![],
             },
+            purged_deleted_files: 0,
             items: None,
         };
         let v = serde_json::to_value(&r).unwrap();

crates/kebab-core/src/traits.rs

@@ -183,6 +183,16 @@ pub trait DocumentStore {
         &self,
         path: &WorkspacePath,
     ) -> anyhow::Result<Option<CanonicalDocument>>;
+
+    /// Return every `workspace_path` stored in the `documents` table.
+    ///
+    /// Used by the post-walker sweep in `kebab-app::ingest` to detect
+    /// documents whose source file has been deleted from the filesystem.
+    /// The set difference `(stored - scanned)` yields orphan candidates;
+    /// each candidate is then existence-checked on disk so that
+    /// out-of-scope files (config narrowing) are NOT purged — only truly
+    /// absent files trigger the purge.
+    fn all_workspace_paths(&self) -> anyhow::Result<Vec<WorkspacePath>>;
 }
 
 pub trait VectorStore {

crates/kebab-store-sqlite/snapshots/ingest_report.snapshot.json

@@ -56,5 +56,6 @@
   "skipped_kebabignore": 0,
   "skipped_size_exceeded": 0,
   "unchanged": 0,
+  "purged_deleted_files": 0,
   "updated": 1
 }

crates/kebab-store-sqlite/src/documents.rs

@@ -352,6 +352,22 @@ impl kebab_core::DocumentStore for SqliteStore {
         }))
     }
 
+    fn all_workspace_paths(&self) -> Result<Vec<kebab_core::WorkspacePath>> {
+        let conn = self.lock_conn();
+        let mut stmt = conn
+            .prepare("SELECT workspace_path FROM documents")
+            .map_err(StoreError::from)?;
+        let rows = stmt
+            .query_map([], |r| r.get::<_, String>(0))
+            .map_err(StoreError::from)?;
+        let mut out = Vec::new();
+        for row in rows {
+            let path = row.map_err(StoreError::from)?;
+            out.push(kebab_core::WorkspacePath(path));
+        }
+        Ok(out)
+    }
+
     fn list_documents(
         &self,
         filter: &kebab_core::DocFilter,

crates/kebab-store-sqlite/src/lib.rs

@@ -35,4 +35,4 @@ pub use error::StoreError;
 pub use eval::{EvalQueryResultRecord, EvalRunRecord, EvalRunRow};
 pub use fts::rebuild_chunks_fts;
 pub use jobs::IngestRunRow;
-pub use store::{CountSummary, NotIndexed, SqliteStore};
+pub use store::{CountSummary, NotIndexed, SqliteStore, purge_deleted_workspace_path};

crates/kebab-store-sqlite/src/store.rs

@@ -540,6 +540,114 @@ pub(crate) fn purge_orphan_at_workspace_path(
     Ok(())
 }
 
+/// Purge all stored data for a document whose on-disk file has been
+/// deleted (as opposed to content-changed, which is handled by
+/// `purge_orphan_at_workspace_path`).
+///
+/// Returns the `chunk_id`s that were associated with the document so
+/// the caller can issue a matching `VectorStore::delete_by_chunk_ids`
+/// on the LanceDB side.
+///
+/// Deletion order:
+/// 1. Collect chunk_ids (before cascade removes them).
+/// 2. DELETE the `documents` row → CASCADE clears `blocks`, `chunks`,
+///    `embedding_records`.
+/// 3. DELETE the `assets` row **only if no other document still
+///    references it** (twin-file protection — `assets` can be shared
+///    across identical-content files via the blake3 PK).
+/// 4. If the asset was `storage_kind = 'copied'`, best-effort delete
+///    the on-disk byte file at `storage_path`.
+///
+/// Returns `Ok(vec![])` when no document exists at `workspace_path`
+/// (idempotent — caller doesn't need to pre-check).
+pub fn purge_deleted_workspace_path(
+    store: &SqliteStore,
+    workspace_path: &kebab_core::WorkspacePath,
+) -> anyhow::Result<Vec<kebab_core::ChunkId>> {
+    let conn = store.lock_conn();
+
+    // Look up the document + its asset_id.
+    let doc_row: Option<(String, String)> = conn
+        .query_row(
+            "SELECT doc_id, asset_id FROM documents WHERE workspace_path = ?",
+            rusqlite::params![workspace_path.0],
+            |r| Ok((r.get(0)?, r.get(1)?)),
+        )
+        .optional()
+        .map_err(StoreError::from)?;
+
+    let Some((doc_id, asset_id)) = doc_row else {
+        return Ok(Vec::new());
+    };
+
+    // 1. Collect chunk_ids before CASCADE removes them.
+    let mut stmt = conn
+        .prepare("SELECT chunk_id FROM chunks WHERE doc_id = ?")
+        .map_err(StoreError::from)?;
+    let rows = stmt
+        .query_map(rusqlite::params![doc_id], |r| r.get::<_, String>(0))
+        .map_err(StoreError::from)?;
+    let chunk_ids: Vec<kebab_core::ChunkId> = rows
+        .map(|r| r.map(kebab_core::ChunkId))
+        .collect::<rusqlite::Result<Vec<_>>>()
+        .map_err(StoreError::from)?;
+    drop(stmt);
+
+    // 2. DELETE the document row (CASCADE clears blocks / chunks /
+    //    embedding_records via the FK constraints in V001).
+    conn.execute(
+        "DELETE FROM documents WHERE doc_id = ?",
+        rusqlite::params![doc_id],
+    )
+    .map_err(StoreError::from)?;
+
+    // 3. Delete the asset row only when no other document still
+    //    references it (twin-file safety: two files with identical
+    //    bytes share a single asset row via the blake3 PK).
+    let remaining_refs: i64 = conn
+        .query_row(
+            "SELECT COUNT(*) FROM documents WHERE asset_id = ?",
+            rusqlite::params![asset_id],
+            |r| r.get(0),
+        )
+        .map_err(StoreError::from)?;
+
+    if remaining_refs == 0 {
+        // 4. Capture storage details before deleting the row.
+        let asset_storage: Option<(String, String)> = conn
+            .query_row(
+                "SELECT storage_kind, storage_path FROM assets WHERE asset_id = ?",
+                rusqlite::params![asset_id],
+                |r| Ok((r.get(0)?, r.get(1)?)),
+            )
+            .optional()
+            .map_err(StoreError::from)?;
+
+        conn.execute(
+            "DELETE FROM assets WHERE asset_id = ?",
+            rusqlite::params![asset_id],
+        )
+        .map_err(StoreError::from)?;
+
+        // 5. Best-effort: remove the on-disk copied asset file.
+        if let Some((storage_kind, storage_path)) = asset_storage {
+            if storage_kind == "copied" {
+                let _ = std::fs::remove_file(&storage_path);
+            }
+        }
+    }
+
+    tracing::debug!(
+        target: "kebab-store-sqlite",
+        workspace_path = %workspace_path.0,
+        doc_id = %doc_id,
+        chunk_count = chunk_ids.len(),
+        "purged deleted-file document from store"
+    );
+
+    Ok(chunk_ids)
+}
+
 /// UPSERT a row into `assets`. Used by both the `put_asset_with_bytes`
 /// path (which has bytes + computed `storage_kind/path`) and the
 /// `DocumentStore::put_asset` path (which only has the `RawAsset` and

crates/kebab-store-sqlite/tests/ingest_report_snapshot.rs

@@ -41,6 +41,7 @@ fn fixture_report() -> IngestReport {
         skipped_generated: 0,
         skipped_size_exceeded: 0,
         skip_examples: kebab_core::SkipExamples::default(),
+        purged_deleted_files: 0,
         items: Some(vec![
             IngestItem {
                 kind: IngestItemKind::New,