> ## Documentation Index > Fetch the complete documentation index at: https://docs.monolex.ai/llms.txt > Use this file to discover all available pages before exploring further. # Monogram Overview > Code intelligence for AI agents and humans — ranked discovery, call graphs, contract audits, and a 50-tool MCP surface across 24 languages. Monogram is Monolex's code-intelligence engine. It turns a source tree into ranked locations, exact symbols, call and dependency graphs, cross-boundary coupling evidence, and deep semantic worklists. The goal is not to guess from a function name; it is to move from a symptom to bounded source evidence and then prove the owning path. *Published contract: `monogram 0.98.11`, OpenCLIs build `2026-07-20-154556`.* Run `monogram --version` to identify the binary you are using. In an agent/non-TTY process, bare `monogram` prints the compact entry brief; use `monogram docs initiate` or `monogram help --full` for the complete embedded reference. ## Quick start ```bash theme={null} # Build or incrementally refresh the current project's index monogram index . # Turn a public requirement into edge bands before searching code monogram spec-audit instruction.md --against . # Bind the ordered task contract, then close it after the final edit and test monogram sequence start "task" --from instruction.md monogram sequence finish current # Locate the implementation, then prove its role monogram search "session reconnect" monogram region "session reconnect lifecycle" -n 5 monogram investigate reconnect_session # Audit bindings that cross language, process, or protocol boundaries monogram coupling --summary # Add the semantic companion for deep graph and possibility-band commands monogram index . --deep monogram semantic status ``` Every investigation result includes executable `[NEXT]` guidance. A normal path is: ```text theme={null} requirement -> spec-audit/sequence -> search/region -> context/investigate -> chain/coupling -> source proof -> change -> rerun the same proof ``` ## Agent entry and embedded docs The `0.98.11` release retains the survivable agent entry introduced in 0.97.0 and keeps the full command manual available on demand: ```bash theme={null} monogram # compact brief when stdout is not a TTY monogram help --full # complete flag-by-flag reference monogram docs # embedded topic inventory monogram docs initiate # complete command reference monogram docs skill # agent workflow and capability map ``` The topic list also includes `audit-guide`, `flow-guide`, `ownership-ffi-guide`, and `sequence`. Human-readable `stats`, `search`, and `region` output routes through a mutation-aware three-state sequence entry gate: * A new recognized task file emits a runnable `sequence start task --from ` hint. Recognized cwd files are `TASK.md`, `PLAN.md`, `BUG.md`, `.task.md`, and `.monobench-task-instruction.md`; the historical `/tmp` Monobench instruction path remains supported. * An open current session initially emits one `ORDER OPEN ()` line naming its `connection-points.md` path and the required final `sequence finish` verb, so a compacted agent can re-enter the binding order. Once a checked file in the saved scope has an mtime newer than the UTC session start, the line escalates to `edits detected in its scope` and the final-close form. * A finished session stays silent for the same task digest, while a different task file triggers the entry hint again. A virgin root with no recognized file retains the generic `sequence start ... --from ` placeholder. `sequence start --from` stores the task's `source_path` and FNV-1a 64-bit identity `source_digest` in `meta.json`. The digest gates duplicate guidance; it is not a cryptographic integrity claim. This release does not add an MCP tool: `monogram mcp-schema` still reports exactly 50 investigation commands. Successful `stats --json`, `search --json`, and `region --json` payloads now include `sequence_hint`: it is the same state-aware edge as a string, or `null` when no edge applies. The MCP server forces those commands through JSON, so MCP clients receive the same field without a second state machine or schema command. The existing `sequence` tool retains its binding `[IAW-SOP] ORDER` chain and closing verb `sequence finish`. `start` and `define` expose that ordered contract in human and JSON output; `status` and `resume` re-emit the current phase after context loss. Run `finish` after the last Edit/Write: it re-presents the saved task contract and available Book knowledge, writes `finish.json`, changes the session phase to `finished`, and tells the agent to make no later source mutation. In 0.98.11, the installed external `initiate.md` and current release source are identical, with SHA-256 `dbb1812866a6291ebc576106ec72a948fb7cdd24f2bd8a1156c9c6d0daa0c963`. The installed SKILL also matches source at `228133b0d369cecbc19150f3b6b20dad76364b6930214c196b7550bff536f627`. The complete hook lifecycle is shipped in this release: ```bash theme={null} monogram hook install # idempotently add the Claude PostToolUse entry monogram hook status # inspect the selected settings file monogram hook remove # remove only Monogram's entry monogram hook install --settings path/to/settings.json ``` The hook preserves unrelated settings and hooks. Its carrier remains a fail-quiet, one-file core-index refresh; it does not build deep semantics, create a database, migrate a schema, or replace an ordinary index refresh. The release also carries forward the Windows-safe ASCII release gate, the synchronized NIIA standalone lock, and the `lib-monosession` optional SQLite boundary required by the all-CLI release gate. `version --json` is not a supported form; use `monogram --version` or `monogram version` for the executing identity. The 0.98.11 CDN metadata has a provenance split. `latest.json` and the Linux and Windows platform rows name clean source commit `04f5162b8bb1518c8814b50de90990ad4030e3ca`; the macOS archive row names clean commit `96d20c623b95e8aa9938b96d2a608557aac09e8d`. Artifact hashes below are verified, but the five rows must not be described as one-source provenance until the release metadata or archive is republished consistently. For isolated CI, benchmark, or disposable-worktree runs, set `MONOGRAM_HOME=`. Core and semantic databases then live under `/monogram/`, while sequence sessions and their `finish.json` witnesses live under `/problem-definitions/`. Without the override, sequence state remains repo-local under `.monogram/problem-definitions/`. Version 0.98.2 closed the earlier leak where sequence artifacts could enter a benchmark Git patch even though the index databases were already isolated; 0.98.11 retains that isolation and the 0.98.3 per-task provenance inside the isolated session. ## What Monogram owns | Plane | Question | Main commands | Detail | | ------------------ | --------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------- | | Contract preflight | What public behaviors and edge bands must the implementation close? | `spec-audit`, `sequence`, `format-trace` | [Reference](/ai-clis/monogram/reference#contract-preflight) | | Locate | Where is the implementation? | `search`, `region`, `symbols`, `grep`, `refgrep` | [Reference](/ai-clis/monogram/reference#locate) | | Navigate | What calls it, what does it call, and where does its value originate? | `context`, `trace`, `investigate`, `chain`, `tree`, `deps`, `rdeps`, `provenance` | [Reference](/ai-clis/monogram/reference#navigate-and-prove) | | Boundary audit | Are HTTP, SQL, event, IPC, FFI, CSS-token, and export/import contracts connected? | `coupling`, `bridges`, `css`, `important` | [Audit & Correctness](/ai-clis/monogram/audit#boundary-and-structural-audits) | | Semantic audit | What does the resolved deep graph observe? | `semantic`, `inspect`, `effect`, `hubs`, `lifecycle`, `unsafe-reach`, `modules`, `injection`, `types` | [Audit & Correctness](/ai-clis/monogram/audit#deep-semantic-plane) | | Possibility bands | Which concrete rows need human or agent proof? | 14 named band/worklist commands | [Audit & Correctness](/ai-clis/monogram/audit#the-14-possibility-band-commands) | | Index estate | Which project database answers, and is it current? | `index`, `reindex`, `stats`, `list`, `scope`, `prune` | [Scope & Index Management](/ai-clis/monogram/scope) | | Boot trace | In what order does a web app initialize? | `boot`, `boot init` | [Boot Sequence Tracer](/ai-clis/monogram/boot) | ## The evidence boundary Monogram deliberately separates observation from conclusion: * Search and region scores rank likely source locations. They do not prove causality. * `uncalled` reports no inbound edge in the indexed graph. Dynamic, reflective, trait, external, and test callers may be invisible. * Deep semantic commands and possibility bands return candidates or complete review worklists. A row is not automatically a defect. * `coupling --verify-callers` reports inbound-edge facts for orphan definitions; public APIs and dynamically invoked handlers still require interpretation. * The stable proof loop is `context` the concrete row, follow it with `chain` or `investigate`, inspect the owning boundary, and rerun the same query after a change. ## Public MCP surface: 50 tools `monogram mcp` exposes 50 investigation tools over stdio JSON-RPC. `monogram mcp-schema` prints the exact wrapper schema used by the server. ```bash theme={null} monogram mcp-schema monogram mcp ``` The 50-tool surface includes locate, navigation, contract, coupling, quality, deep-semantic, and possibility-band commands. The complete inventory and purpose of every tool is in [Monogram Reference](/ai-clis/monogram/reference#complete-50-tool-mcp-inventory). Index and terminal administration are intentionally separate from that 50-tool count. Commands such as `index`, `reindex`, `prune`, `scope`, `docs`, `verify`, `hook claude`, `hook install/remove/status`, and `mcp` manage local state or integration rather than serving as MCP investigation tools. In the sequence family, `start`, `deepen`, `define`, `finish`, and `resume` change repo-local session artifacts; only `status` and `list` are read-only. `boot init` also writes configuration. See the mutation boundaries on the companion pages. ## Supported languages The core index recognizes 24 language families: | Area | Languages and formats | | --------- | ------------------------------------------- | | Systems | Rust, C, C++, Go, Zig | | Web | TypeScript, JavaScript, HTML, CSS, PHP | | Apps | Swift, Kotlin, Dart, Java, Scala | | Scripting | Python, Ruby, Bash/Zsh, Lua | | Config | TOML, YAML, JSON, HCL/Terraform, Dockerfile | The basic index extracts search identifiers, symbols, references, calls, imports, and boundary keys where the language adapter supports them. The deep semantic companion is a separate evidence plane: verify it with `monogram semantic status` before relying on deep commands. ## Project-scoped indexes Each registered project root has its own database. Monogram resolves the deepest indexed ancestor of the current working directory, so your current directory is part of every query. ```bash theme={null} monogram list --health monogram stats --deep ``` In a monorepo, `cd` into the intended indexed subtree before making an absence claim. Learn the registry, workspace expansion, schema-v17 corpus policy, selective recovery, and fail-closed deep-index rules in [Scope & Index Management](/ai-clis/monogram/scope). ## Installation and release identity Monogram is distributed through OpenCLIs: ```bash theme={null} curl -fsSL https://openclis.com/install.sh | sh openclis install monogram openclis update monogram command -v monogram monogram --version openclis info monogram openclis init monogram ``` The installed binary, the OpenCLIs registry entry, and a development checkout can be at different versions. Public behavior should be claimed from the installed release and its live `mcp-schema`; source-only changes are not a shipped feature. The public registry guide includes the ordered sequence flow and relationships to NIIA, Monoflow, Work Wiki, Monograph, the Monogram companion tools, Kernel CLI, and MonoSurf. When command-specific wrapper guidance is useful, run for example `OPENCLIS_NEXT=1 openclis monogram search "session reconnect"`; the wrapper adds a bounded next step after the native Monogram result. The 0.98.11 release has five platform artifacts. Each archive and extracted payload below was downloaded from build `2026-07-20-154556` and verified directly: | Platform key | Archive SHA-256 | Extracted payload SHA-256 | Source commit recorded by platform metadata | | ----------------- | ------------------------------------------------------------------ | ------------------------------------------------------------------ | ------------------------------------------- | | `darwin-aarch64` | `c694b759eac7fa0cc265048c87e158982c9b7a78c0652fbf7d38a32dbcddd9fa` | `e17f019fca556c6185e6f0e594f5d5d35cb7b0c8102347789f1c482b6b6e7d0e` | `96d20c623b95e8aa9938b96d2a608557aac09e8d` | | `linux-x86_64` | `0be4dbafe12608d7c39e630f6aea70078cbfa406c8dba59d64828f341da9059d` | `a6c8b211b4360ce69d84f503d9093a668643d3ab0d7baf07eaf1f7ea3c5d03fd` | `04f5162b8bb1518c8814b50de90990ad4030e3ca` | | `linux-aarch64` | `e974498ec1e24cf9c7494dedfc795556a3135e172582f5b82666f0d8d676dab9` | `35620ca93d50d5e31a0cb645d0a6dfee516d6a5e48911b75392a5e2ca5432fb1` | `04f5162b8bb1518c8814b50de90990ad4030e3ca` | | `windows-x86_64` | `bbc5d2bb43c51988489711ae4e17d961db77e92a806344e99cafcc2e6b356fdb` | `c1debaaf37da5da28e561df4be557679166613a5c75be820d7da69655ac02430` | `04f5162b8bb1518c8814b50de90990ad4030e3ca` | | `windows-aarch64` | `9efb5eacdc97eaf239768dd19fa23c50cca0136b4203974cf64d14c24a00a93a` | `adaf4e923a75de8b43235d3797934574c680d5128ef48d707dd961892dc3cf81` | `04f5162b8bb1518c8814b50de90990ad4030e3ca` | The OpenCLIs-managed macOS payload reports 0.98.11, passes strict signature verification, exposes 50 MCP schema commands, and verifies 353 embedded Book files plus seven initiate-tree files. Archive integrity, executable signature, runtime behavior, and source-provenance metadata are separate proofs; the verified hashes do not resolve the macOS commit split described above. Intel macOS is not part of the stable five-platform matrix. Check `cdn.openclis.com/monogram/latest.json` and its referenced `meta.json` rather than inferring platform support from the Rust source. ## Relationship to the Monolex tools | Tool | Owns | Use together | | ------------------------------------------------- | ------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------- | | [NIIA](/ai-clis/niia) | Work entry, memory, sessions, PTY control, MCP wrapping, OS-control authorization, and remote orchestration | Use NIIA to retain and orchestrate work; use Monogram to prove code structure. | | [Monogram Semantics](/ai-clis/monogram-semantics) | Clean-room structural IR Store, resolved/lexical graphs, effects, and possibility-band evidence | Use Semantics when the product graph needs a deeper source-structure proof plane or an explicit compiler-review lane. | | [Monogram Logos](/ai-clis/monogram-logos) | Three-command MAP/VALIDATE/EMIT foundry over the Semantics Store | Use Logos to review a candidate band before native absorption; use Monogram for the shipped navigation/ranking behavior. | | [Monogram Language](/ai-clis/monogram-language) | Language-self corpus profiles and gated future-prior design artifacts | Use Language for reviewable corpus evidence; it never silently changes Monogram ranking. | | [Monoflow](/ai-clis/monoflow) | Temporal composition across Monogram code structure, git history, documents, watcher events, and saved diffs | Use Monogram for the current code graph; use Monoflow for topics, co-change, gaps, quality delta, and cross-database insight over time. | | [Work Wiki](/ai-clis/work-wiki) | Work history, file biography, project knowledge, and code-to-document convergence | Use Work Wiki to ask whether Monoflow-derived code topics are covered by research and final docs; return to Monogram for symbol and edge proof. | | [Kernel CLI](/kernel-cli) | Local OS observation and action primitives | NIIA owns grants and routes `observe`/`control`; Kernel CLI performs the OS operation. | | [MonoSurf](/monosurf) | Browser connection, observation, and automation | Use MonoSurf for a live web surface and Monogram for the implementation behind it. | | [Monograph](/ai-clis/monograph) | Curated code and fix-shape books | Monogram embeds a release snapshot and can attach Book IDs; the standalone CLI manages and verifies installed Books. | ## Keeping results fresh ```bash theme={null} # Incremental refresh monogram index . monogram search "new symbol" -r # Full, crash-safe rebuild for schema/corpus recovery monogram reindex . ``` `index` and `-r` are the everyday incremental paths. `reindex` is a full rebuild. Monogram prints index identity and freshness before queries; do not silently treat stale results as current evidence. ```text theme={null} ordinary change ──▶ incremental index ──▶ current generation contract epoch changed ────────────────▶ full rebuild required unlisted structural drift ─────────────▶ fail closed; widen the refresh successful reindex ─▶ new current + one rollback margin ─▶ older generations reclaimed ``` Version 0.98.11 separates executable version from extraction compatibility. A different Monogram crate version may continue incremental writes when the stored corpus contract epoch is unchanged; an old contract epoch refuses the write and routes to a rebuild. This avoids needless full rebuilds while still preventing a new extractor from stamping old structural assumptions as current. Selective `--files-from` recovery may converge content or membership drift it observes during the paired core/deep pass. It does not silently accept a new or removed source outside the authoritative carrier: unresolved structural drift leaves semantic currentness closed and requires a broader index. After a successful crash-safe reindex, Monogram protects every live registry pointer, keeps the newest previously served generation as a rollback/in-flight-reader margin, and reclaims older superseded generations plus same-root crash orphans. ## Where next * [Monogram Reference](/ai-clis/monogram/reference) — all 50 MCP tools plus CLI-only integration commands * [Scope & Index Management](/ai-clis/monogram/scope) — database selection, schema-v17 policy, incremental recovery, exclusions, and cleanup * [Audit & Correctness](/ai-clis/monogram/audit) — contract, coupling, semantic, and 14 possibility-band audits * [Boot Sequence Tracer](/ai-clis/monogram/boot) — web initialization order and the config write boundary