backfill: tag commands + file-operations capability

SPEC audit of Phases 12–13 surfaced two gaps. Closing them here so the
v1.1 command surface and capability advertisement match what §12.3 and
§12.4 promise.

Phase 12 — tag commands (§12.3):
- `nuwiki.tags.search` — case-insensitive substring filter over the
  workspace tag index. Returns `[{ name, uri, range, scope, page }]`
  where `scope` is one of `file` / `heading` / `standalone`.
- `nuwiki.tags.generateLinks` — generates/refreshes a tagged-pages
  section. Two modes:
    - `{ uri, tag }` → `= Tag: <name> =` + flat list of `[[Page]]`
      entries for every page tagged with `<name>`.
    - `{ uri }` (no tag) → `= Tags =` umbrella section with `== <tag>
      ==` subgroups, mirroring `:VimwikiGenerateTagLinks` (no arg).
  Idempotent: re-runs replace the existing section by
  case-insensitive heading match.
- `nuwiki.tags.rebuild` — synchronous full re-walk of the wiki root.
  Drops index entries for pages whose files no longer exist on disk,
  re-parses every `.wiki`, and returns `{ pages, files_seen,
  stale_removed }`. Useful for cleaning up after out-of-band edits
  the LSP didn't see.

Ops layer:
- `tag_hits(index, query) → Vec<TagHit>` — pure filter, sorted by
  (name, page, line).
- `tag_pages_snapshot(index) → BTreeMap<tag, [pages]>` — taken under
  the read lock so the dispatcher can release the lock before
  building the edit.
- `build_tag_links_text` / `tag_links_edit` — text-level rendering
  and the WorkspaceEdit producer.

Phase 13 — file-operations capability (§12.4):
- `ServerCapabilities.workspace.file_operations` now advertises
  `did_rename` + `did_delete` with filters scoped to `**/*.wiki`
  and `**/*.md`. (will_* deferred — those return a WorkspaceEdit
  and we'd want to wire them into the rename pipeline before
  promising support.)
- `did_rename_files` handler — moves the live DocumentState forward
  to the new URI when the file was open, then refreshes the index
  (remove old URI, upsert new via read_or_open).
- `did_delete_files` handler — drops both DocumentState and index
  entry so backlink lookups don't surface dangling source URIs.

Tests: 15 new in `phase17_backfill.rs` covering tag hit filtering &
ordering, snapshot dedup, single-tag and full-index render shapes,
edit replace-vs-insert flow, JSON shape of `TagHit`, and the COMMANDS
list. Total 324 tests pass; fmt + clippy clean.

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

crates/nuwiki-lsp/src/commands.rs

@@ -52,6 +52,9 @@ pub const COMMANDS: &[&str] = &[
     "nuwiki.diary.prev",
     "nuwiki.diary.listEntries",
     "nuwiki.diary.openForDate",
+    "nuwiki.tags.search",
+    "nuwiki.tags.generateLinks",
+    "nuwiki.tags.rebuild",
 ];
 
 pub(crate) async fn execute(
@@ -113,6 +116,11 @@ pub(crate) async fn execute(
         "nuwiki.diary.openForDate" => {
             diary_open_for_date(backend, args).map(|o| o.map(CommandOutcome::Value))
         }
+        "nuwiki.tags.search" => tags_search(backend, args).map(|o| o.map(CommandOutcome::Value)),
+        "nuwiki.tags.generateLinks" => {
+            tags_generate_links(backend, args).map(|o| o.map(CommandOutcome::Edit))
+        }
+        "nuwiki.tags.rebuild" => tags_rebuild(backend, args).map(|o| o.map(CommandOutcome::Value)),
         other => Err(format!("unknown nuwiki command: {other}")),
     }
 }
@@ -452,6 +460,128 @@ fn diary_open_for_date(backend: &Backend, args: Vec<Value>) -> Result<Option<Val
     ))
 }
 
+fn tags_search(backend: &Backend, args: Vec<Value>) -> Result<Option<Value>, String> {
+    #[derive(Deserialize, Default)]
+    struct Args {
+        #[serde(default)]
+        uri: Option<Url>,
+        #[serde(default)]
+        query: Option<String>,
+    }
+    let parsed: Args = match args.into_iter().next() {
+        Some(v) => serde_json::from_value(v).map_err(|e| format!("invalid args: {e}"))?,
+        None => Args::default(),
+    };
+    let Some(wiki) = resolve_diary_wiki(backend, parsed.uri.as_ref()) else {
+        return Ok(Some(serde_json::json!([])));
+    };
+    let hits = {
+        let idx = wiki
+            .index
+            .read()
+            .map_err(|_| "index lock poisoned".to_string())?;
+        ops::tag_hits(&idx, parsed.query.as_deref().unwrap_or(""))
+    };
+    Ok(Some(serde_json::to_value(&hits).map_err(|e| {
+        format!("nuwiki.tags.search: serialization failed — {e}")
+    })?))
+}
+
+fn tags_generate_links(
+    backend: &Backend,
+    args: Vec<Value>,
+) -> Result<Option<WorkspaceEdit>, String> {
+    #[derive(Deserialize)]
+    struct Args {
+        uri: Url,
+        #[serde(default)]
+        tag: Option<String>,
+    }
+    let raw = args
+        .into_iter()
+        .next()
+        .ok_or_else(|| "nuwiki.tags.generateLinks: missing { uri } argument".to_string())?;
+    let parsed: Args = serde_json::from_value(raw)
+        .map_err(|e| format!("nuwiki.tags.generateLinks: invalid args — {e}"))?;
+    let doc = match backend.documents.get(&parsed.uri) {
+        Some(d) => d,
+        None => return Ok(None),
+    };
+    let utf8 = backend.use_utf8.load(Ordering::Relaxed);
+    let Some(wiki) = backend.wiki_for_uri(&parsed.uri) else {
+        return Ok(None);
+    };
+    let snapshot = {
+        let idx = wiki
+            .index
+            .read()
+            .map_err(|_| "index lock poisoned".to_string())?;
+        ops::tag_pages_snapshot(&idx)
+    };
+    Ok(ops::tag_links_edit(
+        &doc.text,
+        &doc.ast,
+        &parsed.uri,
+        parsed.tag.as_deref(),
+        &snapshot,
+        utf8,
+    ))
+}
+
+fn tags_rebuild(backend: &Backend, args: Vec<Value>) -> Result<Option<Value>, String> {
+    let p = parse_optional_uri_arg(args)?;
+    let Some(wiki) = resolve_diary_wiki(backend, p.uri.as_ref()) else {
+        return Ok(None);
+    };
+    let registry = std::sync::Arc::clone(&backend.registry);
+    let root = wiki.config.root.clone();
+    if root.as_os_str().is_empty() {
+        return Ok(Some(
+            serde_json::json!({ "pages": 0, "reason": "no wiki root configured" }),
+        ));
+    }
+    let Some(plugin) = registry.get("vimwiki") else {
+        return Err("vimwiki syntax plugin missing".to_string());
+    };
+    let files = crate::index::walk_wiki_files(&root);
+    let total = files.len();
+    let mut indexed = 0usize;
+    let mut idx = wiki
+        .index
+        .write()
+        .map_err(|_| "index lock poisoned".to_string())?;
+    // Drop pages whose files no longer exist. Collect first to avoid mutating
+    // during iteration.
+    let stale: Vec<Url> = idx
+        .pages_by_uri
+        .keys()
+        .filter(|u| match u.to_file_path() {
+            Ok(p) => !p.exists(),
+            Err(_) => true,
+        })
+        .cloned()
+        .collect();
+    for u in &stale {
+        idx.remove(u);
+    }
+    for path in files {
+        let Ok(text) = std::fs::read_to_string(&path) else {
+            continue;
+        };
+        let ast = plugin.parse(&text);
+        let Ok(uri) = Url::from_file_path(&path) else {
+            continue;
+        };
+        idx.upsert(uri, &ast);
+        indexed += 1;
+    }
+    Ok(Some(serde_json::json!({
+        "pages": indexed,
+        "files_seen": total,
+        "stale_removed": stale.len(),
+    })))
+}
+
 fn workspace_find_orphans(backend: &Backend, args: Vec<Value>) -> Result<Option<Value>, String> {
     let p = parse_optional_uri_arg(args)?;
     let wiki = match p.uri.as_ref().and_then(|u| backend.wiki_for_uri(u)) {
@@ -1082,6 +1212,180 @@ pub mod ops {
         b.build()
     }
 
+    // ===== Tag ops (Phase 12 commands) =====
+    //
+    // SPEC §12.3 calls for three tag-driven commands beyond the indexing
+    // that Phase 12 already shipped. `tag_hits` powers `nuwiki.tags.search`;
+    // `tag_links_edit` powers `nuwiki.tags.generateLinks`; the rebuild
+    // command is a direct re-walk of the wiki root in the dispatcher.
+
+    use crate::index::TagOccurrence;
+    use nuwiki_core::ast::TagScope;
+
+    /// One row returned by `nuwiki.tags.search`. Serialised as
+    /// `{ name, uri, range, scope, page }` so editors can render either a
+    /// flat hit list or a per-tag tree.
+    #[derive(Debug, Clone, serde::Serialize)]
+    pub struct TagHit {
+        pub name: String,
+        pub uri: Url,
+        pub range: tower_lsp::lsp_types::Range,
+        pub scope: &'static str,
+        pub page: String,
+    }
+
+    fn scope_tag(s: TagScope) -> &'static str {
+        match s {
+            TagScope::File => "file",
+            TagScope::Heading(_) => "heading",
+            TagScope::Standalone => "standalone",
+        }
+    }
+
+    /// Filter every indexed tag by a case-insensitive substring match. An
+    /// empty query returns everything (sorted by name, then by page).
+    pub fn tag_hits(index: &WorkspaceIndex, query: &str) -> Vec<TagHit> {
+        let needle = query.to_ascii_lowercase();
+        let mut out: Vec<TagHit> = Vec::new();
+        for (name, occs) in &index.tags_by_name {
+            if !needle.is_empty() && !name.to_ascii_lowercase().contains(&needle) {
+                continue;
+            }
+            for occ in occs {
+                let page = index
+                    .pages_by_uri
+                    .get(&occ.uri)
+                    .map(|p| p.name.clone())
+                    .unwrap_or_default();
+                out.push(TagHit {
+                    name: name.clone(),
+                    uri: occ.uri.clone(),
+                    range: no_text_range(&occ.span),
+                    scope: scope_tag(occ.scope),
+                    page,
+                });
+            }
+        }
+        out.sort_by(|a, b| {
+            a.name
+                .cmp(&b.name)
+                .then_with(|| a.page.cmp(&b.page))
+                .then_with(|| a.range.start.line.cmp(&b.range.start.line))
+        });
+        out
+    }
+
+    /// Snapshot of `tag → sorted [page names]` taken under the index read
+    /// lock so the dispatcher can release the lock before computing the
+    /// edit.
+    pub fn tag_pages_snapshot(
+        index: &WorkspaceIndex,
+    ) -> std::collections::BTreeMap<String, Vec<String>> {
+        let mut by_tag: std::collections::BTreeMap<String, std::collections::BTreeSet<String>> =
+            std::collections::BTreeMap::new();
+        for (name, occs) in &index.tags_by_name {
+            for occ in occs {
+                if let Some(page) = index.pages_by_uri.get(&occ.uri) {
+                    by_tag
+                        .entry(name.clone())
+                        .or_default()
+                        .insert(page.name.clone());
+                }
+            }
+        }
+        by_tag
+            .into_iter()
+            .map(|(k, v)| (k, v.into_iter().collect()))
+            .collect()
+    }
+
+    /// Render a `= Tag: <name> =` section listing every page tagged with
+    /// `name`. When `tag` is `None` the section becomes a "Tag Index"
+    /// covering every tag, headed `== <tag> ==` per group — matches
+    /// `:VimwikiGenerateTagLinks` (no arg) variant.
+    pub fn build_tag_links_text(
+        pages_by_tag: &std::collections::BTreeMap<String, Vec<String>>,
+        tag: Option<&str>,
+    ) -> Option<String> {
+        match tag {
+            Some(t) => {
+                let pages = pages_by_tag.get(t)?;
+                if pages.is_empty() {
+                    return None;
+                }
+                let mut out = format!("= Tag: {t} =\n");
+                for p in pages {
+                    out.push_str(&format!("- [[{p}]]\n"));
+                }
+                Some(out)
+            }
+            None => {
+                if pages_by_tag.is_empty() {
+                    return None;
+                }
+                let mut out = String::from("= Tags =\n");
+                for (name, pages) in pages_by_tag {
+                    out.push_str(&format!("\n== {name} ==\n"));
+                    for p in pages {
+                        out.push_str(&format!("- [[{p}]]\n"));
+                    }
+                }
+                Some(out)
+            }
+        }
+    }
+
+    /// Heading name used to locate an existing tag-links section so
+    /// re-generation is idempotent.
+    fn tag_section_heading(tag: Option<&str>) -> String {
+        match tag {
+            Some(t) => format!("Tag: {t}"),
+            None => "Tags".to_string(),
+        }
+    }
+
+    /// Build a `WorkspaceEdit` that replaces an existing `Tag: <name>`
+    /// section (case-insensitive match on the h1 title) or inserts at the
+    /// top of the document when no such section exists. Returns `None`
+    /// when there are no matching tagged pages.
+    pub fn tag_links_edit(
+        text: &str,
+        ast: &DocumentNode,
+        uri: &Url,
+        tag: Option<&str>,
+        pages_by_tag: &std::collections::BTreeMap<String, Vec<String>>,
+        utf8: bool,
+    ) -> Option<WorkspaceEdit> {
+        let body = build_tag_links_text(pages_by_tag, tag)?;
+        let heading = tag_section_heading(tag);
+        let mut b = WorkspaceEditBuilder::new();
+        match find_section_range(ast, &heading) {
+            Some((start, end)) => {
+                let span = Span::new(start, end);
+                b.edit(uri.clone(), text_edit_replace(span, body, text, utf8));
+            }
+            None => {
+                let with_sep = format!("{body}\n");
+                b.edit(
+                    uri.clone(),
+                    text_edit_insert(
+                        LspPosition {
+                            line: 0,
+                            character: 0,
+                        },
+                        with_sep,
+                    ),
+                );
+            }
+        }
+        Some(b.build())
+    }
+
+    // Keep the import live for downstream use even when the local module
+    // doesn't reference it directly.
+    #[allow(dead_code)]
+    fn _retain_tag_occurrence_import(_o: &TagOccurrence) {}
+
     fn whole_doc_span(text: &str) -> Span {
         let bytes = text.as_bytes();
         let mut line = 0u32;

crates/nuwiki-lsp/src/lib.rs

@@ -42,18 +42,21 @@ use tokio::io::{AsyncRead, AsyncWrite};
 use tower_lsp::jsonrpc::Result as LspResult;
 use tower_lsp::lsp_types::{
     CompletionItem, CompletionItemKind, CompletionOptions, CompletionParams, CompletionResponse,
-    Diagnostic, DiagnosticSeverity, DidChangeConfigurationParams, DidChangeTextDocumentParams,
-    DidCloseTextDocumentParams, DidOpenTextDocumentParams, DocumentSymbol, DocumentSymbolParams,
-    DocumentSymbolResponse, ExecuteCommandOptions, ExecuteCommandParams, GotoDefinitionParams,
-    GotoDefinitionResponse, Hover, HoverContents, HoverParams, HoverProviderCapability,
-    InitializeParams, InitializeResult, InitializedParams, Location, MarkupContent, MarkupKind,
-    MessageType, OneOf, PositionEncodingKind, ProgressParams, ProgressParamsValue, ProgressToken,
-    Range, ReferenceParams, RenameParams, SemanticTokens, SemanticTokensFullOptions,
+    DeleteFilesParams, Diagnostic, DiagnosticSeverity, DidChangeConfigurationParams,
+    DidChangeTextDocumentParams, DidCloseTextDocumentParams, DidOpenTextDocumentParams,
+    DocumentSymbol, DocumentSymbolParams, DocumentSymbolResponse, ExecuteCommandOptions,
+    ExecuteCommandParams, FileOperationFilter, FileOperationPattern, FileOperationPatternKind,
+    FileOperationRegistrationOptions, GotoDefinitionParams, GotoDefinitionResponse, Hover,
+    HoverContents, HoverParams, HoverProviderCapability, InitializeParams, InitializeResult,
+    InitializedParams, Location, MarkupContent, MarkupKind, MessageType, OneOf,
+    PositionEncodingKind, ProgressParams, ProgressParamsValue, ProgressToken, Range,
+    ReferenceParams, RenameFilesParams, RenameParams, SemanticTokens, SemanticTokensFullOptions,
     SemanticTokensOptions, SemanticTokensParams, SemanticTokensRangeParams,
     SemanticTokensRangeResult, SemanticTokensResult, SemanticTokensServerCapabilities,
     ServerCapabilities, ServerInfo, SymbolInformation as LspSymbolInformation, SymbolKind,
     TextDocumentSyncCapability, TextDocumentSyncKind, Url, WorkDoneProgress, WorkDoneProgressBegin,
-    WorkDoneProgressEnd, WorkDoneProgressOptions, WorkspaceEdit, WorkspaceSymbolParams,
+    WorkDoneProgressEnd, WorkDoneProgressOptions, WorkspaceEdit,
+    WorkspaceFileOperationsServerCapabilities, WorkspaceServerCapabilities, WorkspaceSymbolParams,
 };
 use tower_lsp::{Client, LanguageServer, LspService, Server};
 
@@ -320,6 +323,10 @@ impl LanguageServer for Backend {
                         },
                     ),
                 ),
+                workspace: Some(WorkspaceServerCapabilities {
+                    workspace_folders: None,
+                    file_operations: Some(wiki_file_operations()),
+                }),
                 ..ServerCapabilities::default()
             },
             server_info: Some(ServerInfo {
@@ -387,6 +394,52 @@ impl LanguageServer for Backend {
         }
     }
 
+    async fn did_rename_files(&self, params: RenameFilesParams) {
+        // Phase 13 advertises this capability so the editor pushes
+        // out-of-band renames (file explorer drags, `:VimwikiRenameFile`
+        // when the client opts to surface the new URI). Update the index
+        // so backlinks/headings track the new URI without waiting for
+        // didOpen on the renamed buffer.
+        for fr in &params.files {
+            let Ok(old_uri) = Url::parse(&fr.old_uri) else {
+                continue;
+            };
+            let Ok(new_uri) = Url::parse(&fr.new_uri) else {
+                continue;
+            };
+            // Pull the live document forward if it was open under the old
+            // URI. Otherwise read the new path from disk and parse.
+            if let Some((_, state)) = self.documents.remove(&old_uri) {
+                self.documents.insert(new_uri.clone(), state);
+            }
+            if let Some(wiki) = self.wiki_for_uri(&new_uri) {
+                let mut idx = wiki.index.write().expect("index lock poisoned");
+                idx.remove(&old_uri);
+            }
+            if let Ok(snapshot) = self.read_or_open(&new_uri).await {
+                if let Some(wiki) = self.wiki_for_uri(&new_uri) {
+                    let mut idx = wiki.index.write().expect("index lock poisoned");
+                    idx.upsert(new_uri.clone(), &snapshot.ast);
+                }
+            }
+        }
+    }
+
+    async fn did_delete_files(&self, params: DeleteFilesParams) {
+        // Mirror of did_rename: drop the index entry so backlink lookups
+        // stop returning the now-missing source URI.
+        for f in &params.files {
+            let Ok(uri) = Url::parse(&f.uri) else {
+                continue;
+            };
+            self.documents.remove(&uri);
+            if let Some(wiki) = self.wiki_for_uri(&uri) {
+                let mut idx = wiki.index.write().expect("index lock poisoned");
+                idx.remove(&uri);
+            }
+        }
+    }
+
     async fn did_close(&self, params: DidCloseTextDocumentParams) {
         let uri = &params.text_document.uri;
         self.documents.remove(uri);
@@ -713,6 +766,43 @@ impl LanguageServer for Backend {
     }
 }
 
+/// File-operation capability for `.wiki` files. Tells the client to
+/// notify us before/after the user renames or deletes files via the file
+/// explorer (or any other out-of-buffer trigger). Filters scope these
+/// notifications to wiki sources so we don't see every C++ rename in a
+/// polyglot workspace.
+fn wiki_file_operations() -> WorkspaceFileOperationsServerCapabilities {
+    let filters = vec![
+        FileOperationFilter {
+            scheme: Some("file".into()),
+            pattern: FileOperationPattern {
+                glob: "**/*.wiki".into(),
+                matches: Some(FileOperationPatternKind::File),
+                options: None,
+            },
+        },
+        FileOperationFilter {
+            scheme: Some("file".into()),
+            pattern: FileOperationPattern {
+                glob: "**/*.md".into(),
+                matches: Some(FileOperationPatternKind::File),
+                options: None,
+            },
+        },
+    ];
+    let opts = || FileOperationRegistrationOptions {
+        filters: filters.clone(),
+    };
+    WorkspaceFileOperationsServerCapabilities {
+        did_create: None,
+        will_create: None,
+        did_rename: Some(opts()),
+        will_rename: None,
+        did_delete: Some(opts()),
+        will_delete: None,
+    }
+}
+
 fn pack_data(flat: &[u32]) -> Vec<tower_lsp::lsp_types::SemanticToken> {
     flat.chunks_exact(5)
         .map(|c| tower_lsp::lsp_types::SemanticToken {