codespine 0.9.9__tar.gz → 1.0.1__tar.gz

codespine-1.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: codespine
+Version: 1.0.1
+Summary: Local Java code intelligence indexer backed by a graph database
+Author: CodeSpine contributors
+License: MIT License
+        
+        Copyright (c) 2026 CodeSpine contributors
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/vinayak3022/codeSpine
+Project-URL: Repository, https://github.com/vinayak3022/codeSpine
+Project-URL: Issues, https://github.com/vinayak3022/codeSpine/issues
+Keywords: java,code-indexing,graph,kuzu,mcp
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Quality Assurance
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: duckdb>=0.10.0
+Requires-Dist: kuzu
+Requires-Dist: tree-sitter
+Requires-Dist: tree-sitter-java
+Requires-Dist: fastmcp>=2.3.0
+Requires-Dist: psutil
+Requires-Dist: watchfiles
+Provides-Extra: ml
+Requires-Dist: sentence-transformers; extra == "ml"
+Requires-Dist: numpy; extra == "ml"
+Provides-Extra: community
+Requires-Dist: igraph; extra == "community"
+Requires-Dist: leidenalg; extra == "community"
+Provides-Extra: full
+Requires-Dist: sentence-transformers; extra == "full"
+Requires-Dist: numpy; extra == "full"
+Requires-Dist: igraph; extra == "full"
+Requires-Dist: leidenalg; extra == "full"
+Dynamic: license-file
+
+# CodeSpine
+
+**v1.0.0** — Local Java code intelligence for coding agents, backed by a graph database.
+
+CodeSpine cuts token burn for coding agents working on Java codebases.
+
+Instead of having an agent open dozens of `.java` files to answer one question, CodeSpine indexes the codebase once and serves the structure over MCP. The agent asks for symbols, callers, impact, flows, dead code, and module boundaries directly — fewer file reads, fewer wasted context windows, fewer hallucinated code paths.
+
+It indexes classes, methods, calls, type relationships, DI bindings, cross-module links, git coupling, dead-code candidates, and execution flows so agents work from graph answers first and source files second.
+
+File changes are written directly to the graph and are immediately queryable — no stale overlay merging, no OOM accumulation. The MCP daemon reloads from an atomic read replica the moment indexing or watch mode completes a batch.
+
+---
+
+## Why It Saves Tokens
+
+- **One MCP call replaces many file opens.** `get_symbol_context("PaymentService")` returns a resolved neighborhood instead of forcing the agent to read every caller and callee file manually.
+- **Search is structure-aware.** Ask for a symbol, concept, impact radius, or dead-code candidate without scanning entire packages.
+- **DI bindings are first-class.** `@Inject`, `@Autowired`, `@Bean`, and `@Provides` edges are resolved and included in impact analysis — Spring and Guice consumers are never missed.
+- **Multi-module repos stay scoped.** Project-aware IDs and `project=` parameters reduce noise from unrelated modules and workspaces.
+- **Repeat sessions get cheaper.** Once indexed, the agent reuses the graph instead of re-discovering the same relationships every turn.
+- **Active edits are visible immediately.** Watch mode writes changes directly to the graph (not a slow overlay), so every MCP query reflects the latest file save.
+- **Natural language dispatch.** `ask("what breaks if I change PaymentService?")` routes to the right tool automatically, reducing agent planning overhead.
+
+---
+
+## Install
+
+```bash
+pip install codespine
+```
+
+Optional semantic search (sentence-transformers):
+
+```bash
+pip install "codespine[ml]"
+```
+
+Everything at once (ml + community detection):
+
+```bash
+pip install "codespine[full]"
+```
+
+### One-time model download (for semantic search)
+
+```bash
+codespine install-model
+```
+
+Downloads and caches the embedding model. Only needed once. After this, `--embed` works without any network access.
+
+---
+
+## Quick Start
+
+```bash
+# 1. Index a project
+codespine analyse /path/to/java-project
+
+# 2. (Optional) Run the expensive deep passes: communities, flows, dead code, coupling
+#    Auto-enabled for repos with ≤ 3,000 files; use --deep to force on larger repos.
+codespine analyse /path/to/java-project --deep
+
+# 3. (Optional) Add semantic embeddings for concept-level search
+codespine analyse /path/to/java-project --embed
+
+# 4. Start MCP server (foreground; your IDE manages the process)
+codespine mcp
+```
+
+Typical output:
+
+```
+$ codespine analyse .
+Walking files...               142 files found
+Index mode...                  incremental (8 files to index, 0 deleted)
+Parsing code...                8/8
+Tracing calls...               847 calls resolved
+Analyzing DI bindings...       63 INJECTS edges, 14 BINDS_INTERFACE edges
+Analyzing types...             234 type relationships
+Cross-module linking...        skipped (single module)
+Detecting communities...       8 clusters found
+Detecting execution flows...   34 processes found
+Finding dead code...           12 unreachable symbols
+Analyzing git history...       18 coupled file pairs
+Generating embeddings...       623 vectors stored
+
+Done in 4.2s — 623 symbols, 1,847 edges, 8 clusters, 34 flows
+Publishing read replica...     MCP will reload automatically
+```
+
+Each analysis phase streams live progress. The final step publishes a read replica so the MCP daemon picks up the new index without restarting.
+
+---
+
+## MCP Configuration
+
+Foreground server:
+
+```bash
+codespine mcp
+```
+
+Minimal `mcp.json` / Claude Desktop config:
+
+```json
+{
+  "mcpServers": {
+    "codespine": {
+      "command": "codespine",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+If the client launches the wrong Python environment, use the absolute binary path:
+
+```json
+{
+  "mcpServers": {
+    "codespine": {
+      "command": "/absolute/path/to/codespine",
+      "args": ["mcp"]
+    }
+  }
+}
+```
+
+### Agent Onboarding
+
+When an agent connects for the first time:
+
+1. **`guide()`** — structured catalog of every tool, by category, with recommended workflows and tips.
+2. **`get_capabilities()`** — what is indexed right now, which features are ready, and what is missing.
+
+The same information is available from the CLI:
+
+```bash
+codespine guide          # tool catalog, workflows, tips
+codespine guide --json   # structured JSON for tooling
+```
+
+---
+
+## MCP Tools (45 total)
+
+### Discovery & Status
+
+| Tool | Description |
+|------|-------------|
+| `guide()` | Tool catalog, workflows, and tips. Call first if new to CodeSpine. |
+| `get_capabilities()` | What is indexed and which features are available right now. |
+| `list_projects()` | All indexed projects with symbol/file counts. |
+| `get_codebase_stats()` | Per-project stats: files, classes, methods, call edges, embeddings. |
+| `list_packages(project)` | Java packages in the index. |
+| `ping()` | Verify the MCP server is alive. |
+
+### Search & Lookup
+
+| Tool | Description |
+|------|-------------|
+| `search_hybrid(query, k, project)` | Ranked symbol search (BM25 + vector + fuzzy via RRF) with `high/medium/low` confidence scores. |
+| `find_symbol(name, kind, project, limit)` | Exact/prefix name lookup; returns `primary_match` flag and disambiguated overloads. |
+| `get_symbol_context(query, max_depth, project)` | One-shot deep context: search + impact + community + flows. |
+| `get_neighborhood(symbol, project)` | Callers (same project), `cross_project_callers` (other projects), callees, siblings, and override/implements links. |
+
+### Analysis
+
+| Tool | Description |
+|------|-------------|
+| `get_impact(symbol, max_depth, project)` | Caller-tree BFS including DI consumers. `self_callers` separates same-class callers from `impacted_callers`. Cached for 5 min. |
+| `find_injections(symbol, project)` | All `@Inject`/`@Autowired` consumers, `@Bean`/`@Provides` providers, and `@Component`/`@Service` implementations. |
+| `detect_dead_code(limit, project, strict)` | Methods with no callers (Java-aware exemptions for tests, contracts, DI entry points). Cached for 5 min. |
+| `trace_execution_flows(entry_symbol, max_depth, project)` | Execution paths from entry points through the call graph. |
+| `get_symbol_community(symbol)` | Architectural community cluster for a symbol. |
+| `get_change_coupling(days, min_strength, min_cochanges)` | Files that changed together in git history (default last 5 days). |
+
+### LLM-Native Tools
+
+Higher-level tools designed to answer full agent questions in a single call, without the agent needing to know which underlying tool to call:
+
+| Tool | Description |
+|------|-------------|
+| `ask(question, project)` | Keyword-based natural language dispatcher: routes "who calls X", "what breaks if Y", "explain Z", "find methods named …" to the right tool automatically. |
+| `what_breaks(symbol, project)` | Plain-English blast-radius summary with `risk_level` (low / medium / high). |
+| `explain(symbol, project)` | What a class or method does and how it fits in the architecture. |
+| `read_symbols(file, symbols, project)` | Extract only the requested method source ranges from a file using tree-sitter — 60–70% token reduction vs. reading the whole file. |
+| `semantic_summary(symbol, project)` | Condensed class view: name, package, extends, implements, public method signatures, annotations. ~80 tokens vs. ~800. |
+| `get_api_surface(class_name, project)` | Public methods and fields only. |
+| `file_context(file_path, project)` | Symbols in a file, callers/callees, community, co-change partners. |
+| `pre_flight_check(file, symbols, change_type)` | Blast-radius check before writing: runs `get_impact` per symbol, returns total affected + risk level + test gap. |
+| `related(symbol, limit, project)` | Symbols structurally related via co-change coupling, shared community, direct calls, or class siblings. |
+| `rename_plan(symbol, new_name, project)` | **Safe cross-project rename plan.** Finds all declaration sites, call sites, and override sites and returns a `files_to_modify` list. No files are modified. |
+| `test_coverage(symbol, project)` | Test methods that cover the given symbol (direct or depth-2 calls from `@Test` methods). |
+| `diff_impact(git_ref, project)` | Graph-level impact analysis for all Java symbols changed since `git_ref`. Returns risk level and per-file affected counts. |
+| `find_pattern(description, project)` | Structural and semantic pattern matching across the codebase. |
+
+### Git
+
+| Tool | Description |
+|------|-------------|
+| `git_log(file_path, limit, project)` | Recent git commits for a path or project. |
+| `git_diff(ref, file_path, project)` | Git diff (working tree vs. ref, or between two refs). |
+| `compare_branches(base_ref, head_ref, project)` | Symbol-level diff between two git refs. |
+
+### Indexing & Watch
+
+| Tool | Description |
+|------|-------------|
+| `analyse_project(path, full, deep, embed)` | Index a Java project (background subprocess). |
+| `get_analyse_status()` | Poll background analysis progress (includes last 30 log lines). |
+| `reindex_file(file_path, project)` | Re-index a single `.java` file (<1 s). Changes are immediately queryable. |
+| `start_watch(path, install_hook)` | Watch for `.java` changes; write directly to graph. Pass `install_hook=True` to also install a post-commit git hook. |
+| `stop_watch()` | Stop the background watch process. |
+| `get_watch_status()` | Watch mode status: running, path, uptime. |
+
+> **Auto-watch:** The MCP server automatically starts watching the most-recently-indexed project on startup if watch is not already running.
+
+### Overlay
+
+| Tool | Description |
+|------|-------------|
+| `get_overlay_status(project)` | Uncommitted overlay state by project/module. |
+| `promote_overlay(project)` | Commit dirty overlay into the base index. |
+| `clear_overlay(project)` | Discard dirty overlay without changing the base. |
+
+### Reset
+
+| Tool | Description |
+|------|-------------|
+| `reset_project(project_id)` | Remove all data for one project. |
+| `reset_index()` | Remove ALL data across every project. |
+| `force_reset_index()` | Emergency: delete data files when normal reset fails. |
+
+### Advanced
+
+| Tool | Description |
+|------|-------------|
+| `run_cypher(query)` | Run a raw Cypher query against the graph DB. |
+
+---
+
+## CLI Reference
+
+```bash
+# Indexing
+codespine analyse <path>                     # incremental index (default)
+codespine analyse <path> --full              # full re-index from scratch
+codespine analyse <path> --deep              # + communities, flows, dead code, coupling
+codespine analyse <path> --incremental-deep  # incremental index + force deep passes
+codespine analyse <path> --embed             # + vector embeddings
+
+# Live watch
+codespine watch --path .                     # file-save-triggered direct-to-graph writes
+codespine watch --path . --install-hook      # also install post-commit git hook
+codespine watch --path . --uninstall-hook    # remove git hook
+
+# Search & Analysis (CLI)
+codespine search "query"                     # hybrid search
+codespine context "symbol"                   # one-shot deep context
+codespine impact "symbol"                    # caller-tree impact (includes DI consumers)
+codespine deadcode                           # dead code candidates
+codespine flow                               # execution flows
+codespine community                          # architectural clusters
+codespine coupling                           # git change coupling
+codespine diff main..feature                 # symbol-level branch diff
+
+# Status & Info
+codespine stats                              # per-project stats (--shards for shard layout)
+codespine list                               # indexed projects
+codespine status                             # service and database status
+codespine guide                              # tool catalog and workflows
+
+# Overlay
+codespine overlay-status                     # dirty overlay state
+codespine overlay-promote                    # commit overlay to base
+codespine overlay-clear                      # discard overlay
+
+# Server Management
+codespine start                              # launch background MCP server (daemon)
+codespine stop                               # stop background MCP server
+codespine mcp                                # foreground MCP (stdio, for IDE clients)
+
+# Model & Setup
+codespine install-model                      # download embedding model for semantic search
+codespine setup                              # check dependencies
+
+# Cleanup & Reset
+codespine clear-project <project_id>         # remove one project
+codespine clear-index                        # remove all indexed data
+codespine force-reset                        # emergency: delete all data files
+```
+
+`analyse` defaults to incremental mode. Repeat runs only process changed files and are fast.
+
+Deep analysis (`--deep`) now runs automatically for repos with ≤ 3,000 files. For larger repos, pass `--deep` explicitly. Use `--incremental-deep` when you want a fast file-only update but still want communities, flows, dead code, and coupling refreshed.
+
+---
+
+## Workspace and Module Detection
+
+CodeSpine can index:
+
+- A single Java repo
+- A multi-module Maven or Gradle project
+- A workspace directory containing multiple independent repos
+
+**Project IDs:**
+
+| Layout | Project ID |
+|--------|------------|
+| Single-module repo | `payments-service` |
+| Multi-module repo: core | `payments-service::core` |
+| Multi-module repo: api  | `payments-service::api` |
+
+Pass the same project ID to any MCP tool or CLI command that accepts `project=` to scope results.
+
+---
+
+## DI / Injection Analysis
+
+CodeSpine resolves dependency injection bindings at index time and stores them as first-class graph edges.
+
+**What is indexed:**
+
+| Annotation | Edge |
+|------------|------|
+| `@Inject` / `@Autowired` field | `INJECTS(consumer → provider, confidence=0.85)` |
+| `@Provides` / `@Bean` method | `INJECTS(config_class → return_type, confidence=0.90)` |
+| `@Component` / `@Service` impl | `BINDS_INTERFACE(impl → interface, confidence=0.95)` |
+
+**Impact on existing tools:**
+
+- `get_impact("PaymentService")` includes classes that inject `PaymentService`, not just direct callers.
+- `detect_dead_code` skips classes that are referenced only via DI edges.
+
+**Dedicated tool:**
+
+```python
+find_injections("PaymentProcessor")
+# → @Inject/@Autowired consumers
+# → @Bean/@Provides providers
+# → @Component/@Service implementations
+```
+
+---
+
+## Instant Change Visibility
+
+CodeSpine writes file changes directly to the graph — no O(N) overlay merge on every query.
+
+When `codespine watch` detects a file save:
+
+1. Parses the changed file with tree-sitter
+2. Atomically clears and re-writes that file's methods, calls, and type relationships
+3. Snapshots the write DB to the read replica
+4. The MCP server picks up the new snapshot on its next tool call
+
+Every tool — `search_hybrid`, `get_impact`, `get_symbol_context`, `find_injections` — reflects the latest file save within the debounce window (default 1–2 s).
+
+### Git Commit Auto Re-index
+
+Watch mode polls `git HEAD` every 5 s. When HEAD changes it runs `git diff --name-only` to find the modified Java files and re-indexes only those — not the full project.
+
+Install an optional post-commit hook so re-indexing fires immediately on every commit:
+
+```bash
+codespine watch --path . --install-hook
+```
+
+Or from MCP:
+
+```python
+start_watch(path=".", install_hook=True)
+```
+
+The hook is idempotent and can be removed:
+
+```bash
+codespine watch --uninstall-hook --path .
+```
+
+---
+
+## Sharding (Multi-Shard Storage)
+
+For large workspaces with many independent projects, CodeSpine distributes project data across multiple on-disk KùzuDB shards using a consistent hash ring.
+
+**Default:** 4 shards stored under `~/.codespine/shards/{0,1,2,3}/db`.
+
+**Key property — module co-location:** All modules of the same project always land on the same shard so cross-module call resolution stays local. `myapp::core` and `myapp::api` always share one shard.
+
+**Parallel indexing:** Projects on different shards are indexed concurrently; modules on the same shard are indexed serially to avoid write contention.
+
+**Configuration:**
+
+```bash
+# Override shard count (applied at first use; changing later requires re-index)
+export CODESPINE_SHARDS=8
+codespine analyse /path/to/project
+```
+
+**Shard topology:**
+
+```bash
+codespine stats --shards
+```
+
+**Programmatic access:**
+
+```python
+from codespine.sharding.store import ShardedGraphStore
+
+sg = ShardedGraphStore(num_shards=4)
+store = sg.shard("my-project")           # returns the right GraphStore shard
+projects = sg.list_project_metadata()    # fan-out across all shards
+```
+
+**Migration from v0.9.x:** On first run after upgrading, `~/.codespine_db` is automatically migrated to shard 0's path (`~/.codespine/shards/0/db`). No manual steps required.
+
+---
+
+## Storage Backends
+
+CodeSpine ships two storage backends.  **DuckDB is the default** starting with v1.0.0.  KùzuDB is retained as the alternate for users who need its property-graph Cypher interface.
+
+### DuckDB (default)
+
+- 10–50× faster batch writes (`executemany` on flat relational tables vs. Kuzu's property-graph MERGE/UNWIND).
+- Single-file database — snapshots are a plain file copy after `CHECKPOINT`.
+- Standard SQL for direct inspection with any DuckDB client or notebook.
+- Transparent Cypher→SQL translation: all analysis modules continue to issue Cypher queries internally; the DuckDB adapter translates them automatically.
+- Bundled in `codespine`'s core dependencies — no extra install step.
+
+### KùzuDB (alternate)
+
+Native property-graph with Cypher.  Prefer this when you need the `run_cypher` MCP tool for ad-hoc traversals or when integrating with other Kuzu tooling.
+
+**Switch to KùzuDB:**
+
+```bash
+CODESPINE_BACKEND=kuzu codespine analyse /path/to/project
+CODESPINE_BACKEND=kuzu codespine mcp
+```
+
+**Per-instance:**
+
+```python
+from codespine.sharding.store import ShardedGraphStore
+
+sg = ShardedGraphStore(backend="kuzu", num_shards=4)    # KùzuDB
+sg = ShardedGraphStore(backend="duckdb", num_shards=4)  # DuckDB (default)
+```
+
+> **Note:** keep `CODESPINE_BACKEND` consistent between the indexer and MCP server for the same shard path — mixing backends on the same path will produce errors.
+
+---
+
+## Result Caching
+
+Expensive analysis tools cache their results for 5 minutes. The cache is keyed by `(tool_name, arguments, snapshot_mtime)` so a new index snapshot automatically invalidates stale entries.
+
+**Cached tools:** `get_impact`, `detect_dead_code`.
+
+The cache is per MCP server instance (in-memory, not persisted across restarts). It is invalidated automatically when `reindex_file` or `analyse_project` completes.
+
+**Cache stats** are visible via `get_capabilities()`.
+
+---
+
+## Deep Analysis Details
+
+The deep analysis phase covers four passes that are expensive but optional:
+
+| Pass | What it does | When to use |
+|------|-------------|-------------|
+| Communities | Detects structural clusters (Leiden algorithm) | Architectural exploration, community tools |
+| Execution flows | Traces call paths from public entry points | `trace_execution_flows`, `get_symbol_context` |
+| Dead code | Finds methods with no callers (Java-aware exemptions) | Cleanup audits |
+| Change coupling | Analyses git history for co-changed file pairs | `get_change_coupling`, `related` |
+
+**Auto-threshold:** deep analysis runs automatically when the project has ≤ 3,000 Java files. Larger repos get lightweight flow/dead-code passes; full deep analysis requires `--deep`.
+
+**Incremental deep:** `--incremental-deep` combines incremental file indexing with a forced full deep pass — useful after large refactors where you want the call graph refreshed quickly but also want updated communities and coupling.
+
+```bash
+codespine analyse . --incremental-deep
+```
+
+**Embeddings** (`--embed`) are independent of deep analysis. Without them, BM25 + fuzzy search still works. Add embeddings when you need concept-level retrieval ("find retry logic", "find payment processing").
+
+---
+
+## Concurrent Indexing and Querying
+
+The indexer (write) and the MCP daemon (read) use separate database paths and buffer pools:
+
+| Path | Pool | Purpose |
+|------|------|---------|
+| `~/.codespine/shards/{N}/db` | 512 MB | Indexer write path |
+| `~/.codespine/shards/{N}/db_read` | 128 MB | MCP + CLI read path |
+
+When indexing completes, the write DB is atomically snapshotted to the read path and a sentinel file is touched. The MCP daemon detects the sentinel change and silently reloads from the new snapshot on the next tool call — no restart needed.
+
+Running `codespine analyse --deep --embed` on one project while querying a different one no longer causes buffer pool OOM or lock contention.
+
+---
+
+## Runtime Files
+
+```
+~/.codespine/
+  shards/
+    0/
+      db/          # Shard 0 write database (KùzuDB directory or DuckDB .db file)
+      db_read/     # Shard 0 read replica
+      db_read.updated  # Sentinel; touched after each snapshot
+    1/ …           # Shards 1-3 (same layout)
+
+~/.codespine.pid               # Background MCP server PID
+~/.codespine.log               # Background server log
+~/.codespine_embedding_cache.json  # Embedding cache (thread-safe JSON)
+~/.codespine_index_meta/       # Incremental file metadata (SHA hashes)
+~/.codespine_overlay/          # Legacy overlay directory (direct-to-graph is primary)
+
+# Legacy paths (pre-0.9.7; auto-migrated to shards/0/ on first run)
+~/.codespine_db/
+~/.codespine_db_read/
+```
+
+---
+
+## Programmatic API
+
+```python
+from codespine.sharding.store import ShardedGraphStore
+from codespine.indexer.engine import JavaIndexer
+from codespine.analysis.impact import analyze_impact
+from codespine.search.hybrid import hybrid_search
+
+# Open (or create) the store
+sg = ShardedGraphStore()
+store = sg.shard("my-project")
+
+# Index a project
+result = JavaIndexer(store).index_project("/path/to/project", full=True, project_id="my-project")
+print(f"Indexed {result.files_indexed} files, {result.methods_indexed} methods")
+
+# Snapshot so readers see the new data
+store.snapshot_to_read_replica()
+
+# Search
+hits = hybrid_search(store, "payment processor", project="my-project")
+
+# Impact analysis
+impact = analyze_impact(store, "PaymentService", max_depth=4, project="my-project")
+```
+
+---
+
+## Notes
+
+- `codespine start` launches a background MCP server. Most IDE MCP clients should use `codespine mcp` instead and manage the process themselves.
+- `codespine watch` writes changes directly to the graph and snapshots the read replica after each batch. MCP queries reflect file saves within the debounce window.
+- `git HEAD` is polled every 5 s. On a new commit, only the changed Java files are re-indexed via `git diff --name-only` — not the full project.
+- `codespine clear-index` rebuilds the local databases from scratch. This also removes the read replicas; run `analyse` again to republish.
+- `codespine force-reset` is the nuclear option — it deletes all data files without going through the DB engine. Use it when `clear-index` fails due to DB corruption (e.g. after an abrupt Ctrl+C mid-write with KùzuDB).
+- For large Spring or JPA-heavy repos, dead-code results should be reviewed before deletion. The tool is conservative by default; use `strict=True` for a more aggressive audit.
+- The `CODESPINE_BACKEND` env var must be set consistently across the indexer and the MCP server — mixing backends on the same shard path will produce errors.
+
+---
+
+## Project Links
+
+- [GitHub](https://github.com/vinayak3022/codeSpine)
+- [Issues](https://github.com/vinayak3022/codeSpine/issues)
+- [PyPI](https://pypi.org/project/codespine/)
+- [Contributing](.github/CONTRIBUTING.md)
+- [Security](.github/SECURITY.md)
+- [Code of Conduct](.github/CODE_OF_CONDUCT.md)