Merge dev into main for gcode 0.7.0 release

Brings in:
- project-#151: tighten gcode project-scoped search (search-symbol,
  --language filter, search-content broadened, scope helpers)
- project-#152: graph enhancements draft (docs)
- project-#153: isolate gcode index roots (IsolationMarker, linked
  worktrees, generated identities, freshness module, --no-freshness)
- project-#154: gcode 0.7.0 release prep (Cargo.toml/lock, CHANGELOG,
  README, user guide, dev guide)
- ghook fix from project-#147 (already tagged ghook-v0.4.1 from dev)

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

Author: joshwilhelmi

CHANGELOG.md

@@ -7,7 +7,30 @@ All notable changes to gobby-cli are documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.4.0] — gobby-hooks
+## [0.7.0] — gcode
+
+### Added
+
+#### gcode
+
+- **`gcode search-symbol` command** — Exact-first symbol/name lookup with deterministic ranking. Resolves precise names ahead of fuzzy matches before falling back to FTS5, and accepts the same `--kind`, `--language`, and `--path` filters as `gcode search`. Use it when you already know (most of) the name and want the canonical hit at rank 0 instead of letting RRF rerank it. (#151)
+- **`--language` filter on search commands** — `search`, `search-symbol`, `search-text`, and `search-content` accept `--language <lang>` to narrow results to a tree-sitter language (e.g. `rust`, `python`, `css`). Composes with `--kind` and `--path`. (#151)
+- **`search-content` covers comments, config, and CSS** — content search now indexes and matches the same comment/config/CSS chunks the indexer already wrote, so doc strings, `*.toml`/`*.yaml`/`*.json` config, and stylesheets are reachable from `gcode search-content`. (#151)
+- **Isolated index roots** — `Context::resolve` now distinguishes five project-identity sources, written up as `ProjectIdentitySource` (`ProjectJson`, `GcodeJson`, `IsolatedRoot`, `LinkedWorktree`, `Generated`):
+  - **Isolation marker** — when `.gobby/project.json` carries `parent_project_path` and/or `parent_project_id`, the directory gets its own filesystem-derived code-index id (UUID5 of the canonical path, namespace `c0de1de0-…`) and is no longer conflated with the parent project. Reading the marker is via the new `project::read_isolation_marker` helper.
+  - **Linked git worktrees** — runs from inside a `git worktree add` directory now resolve to the worktree's own top-level (via `git rev-parse --show-toplevel` + `git worktree list --porcelain` parsing in the new `git` module), and the code-index id is derived from that path rather than from any inherited `.gobby/project.json`. A warning is printed when an inherited id would have been used.
+  - **Generated** — directories without any identity file get a deterministic UUID5 from the canonical path; `.gobby/gcode.json` is only written when `gcode init` runs (via `MissingIdentity::Generate`). Other commands fall back to `MissingIdentity::Error` and ask the user to run `gcode init`.
+- **Read-time freshness checks** — search, symbol, outline, and graph read commands now verify that on-disk source still matches the index before returning results, and incrementally re-index the affected file(s) transparently when they don't. Backed by the new `freshness` module (`FreshnessScope::Project` for project-wide commands, `FreshnessScope::Files` for file-scoped commands like `outline`, plus `ensure_symbol_fresh` for `gcode symbol`). Disable per-call with the new global `--no-freshness` flag, or via `GCODE_FRESHNESS_INFLIGHT=1` for nested processes (a re-entrancy guard so the indexer doesn't recurse into itself). Not a substitute for `gcode index` on bulk changes — intended to keep individual reads honest. (#153)
+- **Project-root walk-up consults git worktree top-level** — `Context::resolve`'s walk-up now prefers `git rev-parse --show-toplevel` (treating linked worktrees as their own top-level) before falling back to generic `.git`/`.hg` markers, so commands invoked deep inside a worktree resolve to the right project root. (#153)
+
+### Changed
+
+#### gcode
+
+- **Project-scoped search and graph commands tightened** — search, symbol, outline, and graph commands now validate that resolved file paths still belong to the current project context before returning results. Stale entries from other projects sharing the same `gobby-hub.db` no longer leak across project boundaries. The new `commands::scope` module owns the path-validation helpers (`normalize_file_arg`, `path_exists_in_current_project`, `indexed_file_exists`, `content_chunks_exist`, `current_indexed_path_is_valid`). (#151)
+- **`gcode init` reports identity source** — init output now distinguishes `initialized`, `existing`, `gobby`, `isolated`, and `linked-worktree` cases when announcing the project context, so it's obvious which identity source resolved.
+
+## [0.4.1] — gobby-hooks
 
 ### Added
 
@@ -22,6 +45,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - **Droid blocking semantics** — droid daemon responses with `continue:false` now exit 2 with the daemon reason while preserving the response JSON on stdout. Other droid block JSON is forwarded on stdout with exit 0 for droid's hook protocol, and daemon transport failures surface as exit 1 stderr diagnostics.
 
+### Fixed
+
+#### gobby-hooks
+
+- **Stop double-emitting Claude PreToolUse denies** — for `--cli=claude`, ghook now narrows the legacy `stderr+exit(2)` channel to daemon responses that explicitly set top-level `continue:false` with a non-empty `stopReason` (the HARD_STOP shape). All other responses — including PreToolUse denies that arrive via `hookSpecificOutput.permissionDecision:"deny"` — are emitted as JSON on stdout with exit 0, matching the structured-channel contract the Python `ClaudeCodeAdapter` already targets. Previously, ghook synthesized a second deny channel on top of the structured one, causing Claude Code to render every PreToolUse deny twice (once as a permission denial, once as a "hook blocking error"). Codex/Gemini/Qwen/Droid paths are unchanged.
+
 ## [0.3.1] — gobby-hooks
 
 ### Added

Cargo.lock

@@ -1,6 +1,6 @@
 [package]
 name = "gobby-code"
-version = "0.6.2"
+version = "0.7.0"
 edition = "2024"
 rust-version = "1.85"
 authors = ["Josh Wilhelmi <hello@gobby.ai>"]

crates/gcode/Cargo.toml

@@ -105,9 +105,12 @@ gcode init
 # Search
 gcode search "query"                      # Hybrid: FTS + semantic + graph boost
 gcode search "query" --kind function      # Filter by symbol kind
+gcode search "query" --language rust      # Filter by source language
 gcode search "query" --path "src/**/*.rs" # Filter by file path glob
+gcode search-symbol "outline"             # Exact-first symbol/command lookup
+gcode search-symbol "outline" --kind function --language rust
 gcode search-text "query"                 # FTS5 on symbol names/signatures
-gcode search-content "query"              # FTS5 on file content
+gcode search-content "query"              # FTS5 on file content, comments, config, CSS
 
 # Symbol retrieval
 gcode outline src/auth.ts                 # Hierarchical symbol tree
@@ -138,6 +141,7 @@ gcode search --project /path/to/app "q"   # By path
 # Global flags
 --format text|json                        # Output format (default: json)
 --quiet                                   # Suppress warnings and progress
+--no-freshness                            # Skip read-time index/source freshness checks
 ```
 
 ## Standalone vs Gobby

crates/gcode/README.md

@@ -1,5 +1,3 @@
-use gobby_core::project::{find_project_root, read_project_id};
-
 use crate::config::Context;
 use crate::db;
 use crate::index::indexer;
@@ -15,23 +13,28 @@ pub fn run(
     let (root, project_id, conn) = match path.as_deref() {
         Some(p) => {
             let target = std::path::PathBuf::from(p);
-            let target_root = find_project_root(&target).unwrap_or_else(|| target.clone());
+            let target_root = crate::config::detect_project_root_from(&target)?;
             if target_root != ctx.project_root {
                 // Path belongs to a different project — re-resolve everything
                 let db_path = crate::config::resolve_db_path(&target_root)?;
-                let project_id = read_project_id(&target_root)
-                    .or_else(|_| crate::project::read_gcode_json(&target_root))
-                    .unwrap_or_else(|_| crate::project::generate_project_id(&target_root));
+                let identity = crate::config::resolve_project_identity(
+                    &target_root,
+                    crate::config::MissingIdentity::Generate,
+                )?;
+                crate::config::warn_project_identity(&identity, ctx.quiet);
                 if !ctx.quiet {
                     eprintln!(
                         "Warning: path '{}' belongs to project {} (not {}), re-resolving context",
                         p,
-                        &project_id[..8],
+                        short_id(&identity.project_id),
                         &ctx.project_id[..8]
                     );
                 }
                 let conn = db::open_readwrite(&db_path)?;
-                (target_root, project_id, conn)
+                if identity.should_write_gcode_json {
+                    crate::project::ensure_gcode_json(&target_root)?;
+                }
+                (target_root, identity.project_id, conn)
             } else {
                 let conn = db::open_readwrite(&ctx.db_path)?;
                 (target, ctx.project_id.clone(), conn)
@@ -43,9 +46,6 @@ pub fn run(
         }
     };
 
-    // Auto-init: ensure identity file exists before indexing
-    crate::project::ensure_gcode_json(&root)?;
-
     if let Some(file_list) = files {
         let result = indexer::index_files(&conn, &root, &project_id, &file_list)?;
         if !ctx.quiet {
@@ -69,3 +69,7 @@ pub fn run(
 
     Ok(())
 }
+
+fn short_id(id: &str) -> &str {
+    id.get(..8).unwrap_or(id)
+}

crates/gcode/src/commands/index.rs

@@ -8,14 +8,21 @@ use crate::project;
 use crate::skill;
 
 pub fn run(project_root: &Path, format: Format, quiet: bool) -> anyhow::Result<()> {
-    let (project_id, was_created) = project::ensure_gcode_json(project_root)?;
-
-    let status = if was_created {
-        "initialized"
-    } else if project_root.join(".gobby").join("project.json").exists() {
-        "gobby"
+    let identity =
+        config::resolve_project_identity(project_root, config::MissingIdentity::Generate)?;
+    config::warn_project_identity(&identity, quiet);
+    let (project_id, was_created) = if identity.should_write_gcode_json {
+        project::ensure_gcode_json(project_root)?
     } else {
-        "existing"
+        (identity.project_id.clone(), false)
+    };
+
+    let status = match identity.source {
+        config::ProjectIdentitySource::IsolatedRoot => "isolated",
+        config::ProjectIdentitySource::LinkedWorktree => "linked-worktree",
+        config::ProjectIdentitySource::ProjectJson => "gobby",
+        config::ProjectIdentitySource::Generated if was_created => "initialized",
+        _ => "existing",
     };
 
     // Detect AI CLIs and install skills (skip if gobby manages this project)
@@ -81,6 +88,14 @@ pub fn run(project_root: &Path, format: Format, quiet: bool) -> anyhow::Result<(
                             project_root.display()
                         );
                     }
+                    "isolated" | "linked-worktree" => {
+                        eprintln!(
+                            "Using {} code index: {} ({})",
+                            status,
+                            project_id,
+                            project_root.display()
+                        );
+                    }
                     _ => {
                         eprintln!(
                             "Already initialized: {} ({})",

crates/gcode/src/commands/init.rs

@@ -1,6 +1,7 @@
 pub mod graph;
 pub mod index;
 pub mod init;
+pub(crate) mod scope;
 pub mod search;
 pub mod status;
 pub mod symbols;