feat: add code-navigation tools (grep, glob, ls) + read_file line ranges (#1670)

Gives the agent first-class code navigation instead of shelling out via bash
(token-heavy, unreliable on weaker models, unstructured). Mirrors the
Grep/Glob/Read primitives that Claude Code / opencode expose.

- grep: regex search over file contents across a tree. Uses ripgrep when
  available (with explicit excludes so junk dirs are skipped even without a
  .gitignore); falls back to a pure-Python walk+regex when rg is absent.
  Returns file:line:match, capped.
- glob: find files by glob pattern (recursive), newest first.
- ls: list a directory (folders first, then files with sizes).
- read_file: optional offset/limit for line-range reads of large files
  (plain-path calls stay back-compatible).

All confined by the same path policy as read_file (_resolve_tool_path:
data/tmp allowlist + sensitive-file deny). Junk dirs (.git, node_modules,
venv, __pycache__, dist/build, …) skipped. Output capped (200 hits,
400 chars/line). Admin-gated like the other filesystem tools.

Wiring: schemas + native arg->content serializer (src/tool_schemas.py), tool
tags (src/agent_tools.py), always-available + descriptions (src/tool_index.py),
admin gate (src/tool_security.py), dispatch + impls (src/tool_execution.py).

Tests: tests/test_code_nav_tools.py — match/skip-junk/ignore-case/glob-filter,
allowlist rejection, glob/ls, read-range, and the no-ripgrep Python fallback.

src/tool_index.py

@@ -23,6 +23,7 @@ logger = logging.getLogger(__name__)
 # These are the most commonly needed and should never be missing.
 ALWAYS_AVAILABLE = frozenset({
     "bash", "python", "web_search", "web_fetch", "read_file",
+    "grep", "glob", "ls",  # code-navigation tools (admin-gated by tool_security)
     "api_call",  # For configured integrations (Miniflux, Gitea, Linkding, etc.)
     # The two genuinely AMBIENT cookbook tools — "what's running" and
     # "kill it" can be asked any time without prior cookbook context,
@@ -63,7 +64,10 @@ BUILTIN_TOOL_DESCRIPTIONS: Dict[str, str] = {
     "python": "Execute Python code for computation, data processing, math, scripting, parsing, API calls. Not for writing code for the user.",
     "web_search": "Quick single web lookup for a fact, current event, or doc mid-task. NOT for 'research X' / 'do research on X' requests — those are deep-research jobs (use trigger_research). web_search = one query; trigger_research = a full researched report in the sidebar.",
     "web_fetch": "Fetch and read the text content of a specific URL/website the user names (e.g. 'check example.com', 'open this link'). Use when you have a concrete URL; for open-ended lookups use web_search instead.",
-    "read_file": "Read a file from disk and return its contents. View source code, config files, logs.",
+    "read_file": "Read a file from disk and return its contents. View source code, config files, logs. Supports an optional line range (offset/limit) for large files.",
+    "grep": "Search file CONTENTS for a regex across a directory tree (ripgrep-backed, honours .gitignore). Returns file:line:match. Use to find where code/symbols/strings live — prefer over bash grep.",
+    "glob": "Find FILES by glob pattern (e.g. '**/*.py'), newest first. Use to locate files by name/extension — prefer over bash find/ls.",
+    "ls": "List a directory's entries (folders then files with sizes). Use to see what's in a folder — prefer over bash ls.",
     "write_file": "Write/create or fully rewrite a file ON DISK (source code, configs, project files). Use for new files or full rewrites — NOT create_document (editor panel) and NOT a bash heredoc.",
     "edit_file": "Edit an existing file ON DISK by exact string replacement (fix a bug, change a function). Shows a diff. The tool for changing files on disk — NOT edit_document (editor panel) and NOT bash sed/heredoc.",
     "create_document": "Create a new document in the editor panel. For code, articles, text content longer than 15 lines, unless an already-open document/email draft is the obvious target. If an email compose draft is open, edit that draft instead of creating another document.",