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@spechycom/archon\n\n**A deterministic context compiler for AI coding agents.**\n\nYour project knowledge lives in a DAG of small, single-purpose documents\ninstead of one giant `CLAUDE.md`. The agent says *\"I'm about to touch\n`src/api/users.ts`\"* — archon returns exactly the rules wired to that path,\nnothing else, over MCP. Same request + same knowledge version = same bytes,\nevery time.\n\n🇹🇷 [Türkçe README](./README.tr.md)\n\n---\n\n## Contents\n\n| | |\n|---|---|\n| **Get started** | [Why](#why) · [How it works](#how-it-works) · [Quick start](#quick-start) · [Installation](#installation) · [Building the knowledge base](#building-the-knowledge-base) |\n| **Daily use** | [What a session looks like](#what-a-session-looks-like) · [Capturing decisions](#capturing-decisions-standing-rules) · [Team workflows](#team-workflows) |\n| **Reference** | [Tools — agent surface](#tools--agent-surface) · [Tools — admin surface](#tools--admin-surface) · [CLI](#cli) · [Prompts & resources](#prompts--resources) |\n| **Concepts** | [Knowledge model](#knowledge-model) · [Delivery budget](#delivery-budget) · [Determinism](#determinism) |\n| **Beyond the DAG** | [Semantic embeddings](#semantic-embeddings) · [Code awareness](#code-awareness) · [Episodic memory](#episodic-memory) · [Document discovery](#document-discovery) · [Graph visualization](#graph-visualization) · [Quality tooling](#quality-tooling) |\n| **Plumbing** | [Editor adapters](#editor-adapters) · [Hooks](#hooks) · [Agent Skills](#agent-skills) · [Status & limitations](#status--limitations) · [Development](#development) |\n\n---\n\n## Why\n\nA single instruction file (`CLAUDE.md`, `.cursorrules`, `AGENTS.md`) has\nthree failure modes, and archon is built against each one:\n\n| Single-file failure | What archon does instead |\n|---|---|\n| Every rule rides in every prompt, most of them irrelevant | Only documents *reachable* from the target files are compiled |\n| Token cost grows with the file, forever | An allocator inlines what fits and defers the rest as file references |\n| No record of what the agent actually read | Every compile is written to an audit log, queryable by `compile_id` |\n\nThe core retrieval path is **deliberately dumb**: no embeddings, no LLM, no\nrandomness — four resolution steps over SQLite. Everything smarter (semantic\nsuggestions, symbol graphs, episodic memory) is layered *on top* as additive,\nfail-open extras that can never change or break the deterministic result.\n\n## How it works\n\n`compile_context` resolves the target files against the knowledge DAG in\nfour deterministic steps:\n\n```\ntarget_files ──▶ 1. path_requires     glob match (picomatch) per file\n                 2. layer_requires    file → layer (layer_rules) → docs\n                 3. command_requires  exact match on the `command` argument\n                 4. doc_depends_on    transitive closure over matched docs\n                        │\n                        ▼\n                 ordering: specificity ↓, priority ↑, doc_id ↑\n                        │\n                        ▼\n                 intent_tags expansion (optional, additive)\n                        │\n                        ▼\n                 relevance filter (optional, needs `plan`)\n                        │\n                        ▼\n                 delivery allocator → inline / deferred / omitted\n                        │\n                        ▼\n                 audit row + snapshot_id + knowledge_version\n```\n\nThe read path only ever sees `status = 'approved'` rows, and cycles in\n`doc_depends_on` are rejected at insert time — step 4 always terminates.\n\n## Quick start\n\n1. **Run the setup wizard from your project root:**\n\n   ```bash\n   npx @spechycom/archon@latest setup\n   ```\n\n   Interactive, no flags to memorize: pick your agent(s) (Claude Code,\n   Cursor, Codex), it registers both MCP servers for you (`archon` agent\n   surface + `archon-admin`), detects your stack and previews a knowledge\n   template (or starts empty), deploys the editor adapters, and offers an\n   optional local-embeddings step. One command, one screen at a time, a\n   summary before anything is written.\n2. **Keep coding normally.** The wizard already deployed the editor\n   adapters: `CLAUDE.md` / `AGENTS.md` / Cursor rules now instruct the\n   agent to call archon before touching any file. You never call a tool by\n   hand.\n3. **Run the same command again any time to update.** An existing\n   `.spechy/` is detected automatically and the wizard switches to update\n   mode — version bump, template upgrade, adapter redeploy, symbol\n   reindex, and (if enabled) an embeddings refresh, all idempotent.\n\nRequires Node.js >= 18. Windows is supported — the wizard is written to\nbehave the same in PowerShell/cmd.exe as in a POSIX shell — but it's new\nand hasn't had a field validation pass yet; if something looks wrong,\nplease [file an issue](https://github.com/spechycom/archon/issues). The\nSQLite database is created and migrated on first start — plain\nDELETE-journal mode, one `.db` file, no `-wal`/`-shm` sidecars.\n\nCan't or don't want to run the wizard (CI, a locked-down shell, hand\ncontrol over every file)? See [Manual installation](#manual-installation)\nbelow — it's the same result, one step at a time.\n\n## Installation\n\nTwo surfaces, deliberately two separate MCP server processes:\n\n- **agent** — read-only, cannot mutate knowledge. 9 tools. This is what\n  your coding agent gets.\n- **admin** — everything including the write path, 37 tools total. Keep it\n  away from the coding agent's session: an agent holding\n  `spechy_approve_proposal` can approve its own proposals, which defeats\n  the human-approval boundary (P-3, INV-6).\n\nThe split is enforced twice: admin tools are *not registered* on the agent\nsurface (invisible to `tools/list`, \"unknown tool\" at the protocol level),\nand every admin service method independently asserts the surface as its\nfirst statement — even a caller bypassing the MCP server entirely cannot\nmutate canonical knowledge from the agent surface.\n\nAlways pass `--project-root` explicitly: an MCP client's cwd is not\npredictable, and `file_path` imports are sandboxed to this root.\n\nThe `setup` wizard (see [Quick start](#quick-start)) does everything below\nfor you — registration for both surfaces, per-client. Read on only if you\nwant to do it by hand, or the wizard isn't an option in your environment.\n\n### Manual installation\n\n### Claude Code\n\n**Option 1 — edit `.mcp.json`** (project root; for Cursor the same JSON\ngoes in `.cursor/mcp.json`):\n\n```jsonc\n// .mcp.json — only the agent surface belongs here\n{\n  \"mcpServers\": {\n    \"archon\": {\n      \"command\": \"npx\",\n      \"args\": [\n        \"-y\", \"@spechycom/archon\",\n        \"--surface\", \"agent\",\n        \"--db\", \".spechy/archon.db\",\n        \"--project-root\", \"/absolute/path/to/project\"\n      ]\n    }\n  }\n}\n```\n\nCommit this file — that's what MCP's `project` scope is for. **Do not add\n`archon-admin` to `.mcp.json`**: the file has no per-agent scoping, so\nevery server in it connects to the coding agent's session. The admin entry\ngoes in your personal (`local`) scope instead:\n\n```bash\nclaude mcp add-json archon-admin '{\n  \"command\": \"npx\",\n  \"args\": [\"-y\", \"@spechycom/archon\", \"--surface\", \"admin\", \"--db\", \".spechy/archon.db\", \"--project-root\", \"'\"$PWD\"'\"]\n}' --scope local\n```\n\n**Option 2 — CLI for both**: same `claude mcp add-json` shape with\n`--scope project` for `archon` (agent). Run `/mcp` inside Claude Code\nafterwards to confirm both servers connected.\n\n(Context cost of mounting admin anyway is small where tool schemas load on\ndemand — measured once at ~426 tokens — so keep it out for the boundary,\nnot the tokens.)\n\n### Codex\n\n```bash\ncodex mcp add archon -- npx -y @spechycom/archon --surface agent --db .spechy/archon.db --project-root \"$PWD\"\ncodex mcp add archon-admin -- npx -y @spechycom/archon --surface admin --db .spechy/archon.db --project-root \"$PWD\"\n```\n\nOr write the same two entries into `~/.codex/config.toml` directly. Codex\nhas no per-agent scoping either — only add `archon-admin` where you control\nwho drives the session. `codex mcp list` confirms registration.\n\n### Windows\n\n`\"$PWD\"` is bash/zsh syntax. On Windows, edit `.mcp.json` /\n`config.toml` directly (plain JSON/TOML, no shell involved) and use forward\nslashes in `--project-root` (`C:/Users/you/project`) — Node resolves them\nfine and you skip `\\\\` escaping. From PowerShell, `\"$($PWD.Path)\"` replaces\n`\"$PWD\"`; from `cmd.exe`, paste the absolute path literally. WSL counts as\nLinux.\n\n### Flags\n\n| Flag | Default | Notes |\n|---|---|---|\n| `--surface` | `agent` | `agent` or `admin` |\n| `--db` | `.spechy/archon.db` | Relative paths resolve against `--project-root`; parent dir auto-created |\n| `--project-root` | `process.cwd()` | Always pass it explicitly |\n| `--templates` | — | Overrides the local templates directory used by the `init_*` tools |\n\n## Building the knowledge base\n\nThree entry points, by what you're starting from:\n\n### A — new project, bootstrap from a template\n\nPackaged templates: **Laravel**, **Next.js**, **Python**, **Go** (the last\ntwo match on language alone). Vite is recognized as a signal but has no\nbundled template yet. Via the admin surface:\n\n1. `spechy_init_detect` — read-only: inspects manifests\n   (`package.json`, `composer.json`, …) and directory shape, scores the\n   templates, returns a preview + `preview_hash`. Optional `placeholders`\n   override template values (Next.js `app_root` is auto-detected between\n   `src/app`/`app`). No fit, or empty on purpose → `skip_template: true`.\n2. `spechy_init_confirm({ preview_hash })` — bootstraps canonical knowledge\n   from the previewed template and deploys the editor adapters. The hash is\n   process-scoped; a stale one is rejected.\n3. Add your real project rules with `spechy_import_doc` (see C), then\n   verify with one `spechy_compile_context` call against a covered path.\n\nThe `spechy-setup` [Agent Skill](#agent-skills) walks an agent through\nexactly this.\n\n### B — existing docs to migrate\n\nDon't init from a template — bulk-import what you have. The\n`spechy-bulk-import` [Agent Skill](#agent-skills) drives the analyze\npipeline: `spechy_analyze_import_batch` splits each file into import units\nby `##` heading and infers `kind`/`edge_hints`,\n`spechy_execute_import_plan` turns the reviewed plan into pending proposals\nsharing one `bundle_id`, and `spechy_approve_proposal_bundle` lands the\nwhole batch as a single snapshot. Nothing enters canonical knowledge\nwithout that approval step.\n\n### C — one document at a time\n\n```json\n{\n  \"doc_id\": \"api-constraint\",\n  \"title\": \"API layer constraints\",\n  \"kind\": \"constraint\",\n  \"content\": \"Never call fetch directly from components. Always go through src/api/client.ts.\",\n  \"edge_hints\": [{ \"edge_type\": \"path_requires\", \"source_value\": \"src/api/**\" }]\n}\n```\n\n`spechy_import_doc` (admin) with inline `content` or a repo-relative\n`file_path`. Write documents **small and single-purpose** — a document is\nthe unit of retrieval, so one covering three topics gets pulled in for all\nthree. The tool warns above 4096 bytes, at 2+ `##` headings, and when no\n`edge_hints` are given (an edge-less document is unreachable from any\ncompile). Re-importing a `doc_id` overwrites content but *accumulates*\nedges. A fresh database tells you so: `compile_context` returns a\n\"Project not initialized\" warning instead of silently returning nothing.\n\nAlternatively, keep rules in a YAML seed file (`documents[]` with\n`file`/`patterns`/`depends_on`, plus `layer_rules[]`) committed to git:\n\n```bash\nspechy-archon seed spechy.seed.yaml\n```\n\n## What a session looks like\n\nYou don't call tools yourself — the deployed adapter text instructs the\nagent. What that adds up to, scenario by scenario:\n\n**Before touching a file** the agent calls `spechy_compile_context` with\nthe files and a one-line plan, reads what comes back `inline`, opens\n`deferred` documents' `source_path` itself, and obeys `notices`.\n\n**\"Did this change break a written rule?\"** — `spechy_verify_done` with the\nsession's diff mechanically checks changed files against every approved\n`constraint` carrying a ` ```verify ` YAML block (`forbid_import`,\n`require_companion`), and suggests likely-affected test files. No human has\nto spot the violation first.\n\n**\"What does changing these files touch?\"** — `spechy_impact({ files })`\nlists every approved document the DAG maps those files to, with the exact\nedge as evidence. It answers *which rules apply*; `verify_done` answers\n*was a rule broken*.\n\n**\"How does the code get from A to B?\"** — `spechy_search_logic_flow`\nBFS-searches the tree-sitter call graph for the shortest call path between\ntwo symbols. See [Code awareness](#code-awareness).\n\n**\"Didn't we try this before?\"** — `spechy_recall` returns past runs:\nfiles touched, plans, session notes. Never injected automatically — asked\nfor when the work has a past. `compile_context`'s notices independently\nflag failed/reverted attempts from the last 90 days on the same files.\n\n**The agent missed a rule you know exists** — it (or you) files\n`spechy_observe` with `event_type: \"compile_miss\"`; a wrong-content rule\ngets `\"review_correction\"`. Neither touches canonical knowledge — an admin\ntriages later (`spechy_process_observations` → proposals → approve/reject).\nThe `spechy-triage` [Agent Skill](#agent-skills) has the decision tree.\n\n**Reviewing / scaffolding / explaining** — the three bundled\n[prompts](#prompts--resources) cover \"review these files against their\nrules\", \"scaffold with template documents included\", and \"explain the rules\nfor this file to a human\".\n\n**A doc's source file drifted** — `spechy_sync_docs` (admin) checks\nfile-anchored documents against their sources and opens an `update_doc`\nproposal per drifted one; `dry_run: true` previews.\n\n**A packaged template got a new version** — `compile_context` notices tell\nyou proactively; `spechy_check_upgrade` shows the diff,\n`spechy_apply_upgrade` turns it into pending proposals (never overwriting\ndocuments you've modified), and `spechy_sync_init_manifest` re-baselines\nafter the bundle is resolved — skip that last call and the same upgrade is\noffered forever.\n\n**Health checks** — `spechy_workspace_status` for a read-only dashboard;\n`spechy-archon doctor` for the full scan (isolated docs, dead edges,\nmissing/stale sources, cycles, oversized docs, near-duplicate rules,\nco-change suggestions).\n\n## Capturing decisions (standing rules)\n\nTell the agent something meant to outlive the turn — \"from now on, don't\nrun tests unless I say so\" — and the adapter text has it call\n`spechy_observe` with `event_type: \"manual_note\"` and ask you to confirm.\nYour **next prompt** commits it: the `UserPromptSubmit` hook reads your\nreply, and a confirmation approves the rule into the knowledge base and\nwrites it to **`.spechy/rules.md`** — a plain-text, git-tracked catalogue\nyou can read or hand-edit (run `sync-rules-file` after editing directly).\nApproving the same proposal from the admin surface lands in the same place.\n\nIf the new rule collides with an existing one, `observe` returns\n`conflict_candidates` and the agent offers *keep both / replace / cancel* —\npersisted via `spechy_resolve_conflict`.\n\nTo retire a decision outright, call `spechy_delete_decision` (admin\nsurface) with its `doc_id` — no counter-rule or conflict dance needed. It\nis a soft-delete: the rule is deprecated (its edges follow, the knowledge\nversion bumps, a snapshot is written) and disappears from every compile,\nbut the record stays in history and snapshots. There is deliberately no\nhard-delete: snapshots are immutable (INV-3).\n\nRules scoped to a file/layer/command come back through normal compiles.\nBehaviour rules with no file to attach to are never loaded unconditionally:\nthe hook matches your prompt's wording against each rule and injects only\nwhat looks relevant — deliberately noise-limited (a rule already mentioned\nthis session isn't re-injected, and there's a hard per-session cap).\n\n## Team workflows\n\nCheapest first:\n\n- **Standing rules sync for free** — commit `.spechy/rules.md`. A teammate\n  who pulls picks the rules up on their next session; the hook absorbs\n  whatever's on disk into its own database before rendering over it, so a\n  pulled rule is never silently lost.\n- **Commit a `spechy.seed.yaml`**, everyone runs `spechy-archon seed` after\n  pulling — reviewable as a normal PR diff. Best for structural knowledge.\n- **`spechy-archon export <file>` / `import <file>`** — portable JSON\n  snapshot of the whole database. One-off syncs, pre-risky-operation\n  backups, machine moves. `import` fully replaces the target DB.\n- **Rebuild per environment** from the same sources (`spechy-bulk-import`).\n- **Commit the `.db` itself** as a last resort — works, but every pull that\n  changes it swaps the file under the running server (which reopens the\n  connection by itself, at the cost of one warning-carrying compile).\n\nIf the team diverges (`knowledge_version` mismatch), compiles stop matching\nbetween people — see [`docs/TROUBLESHOOTING.md`](./docs/TROUBLESHOOTING.md).\nMore role-by-role workflows: [`docs/USAGE.md`](./docs/USAGE.md).\n\n## Tools — agent surface\n\nTool names take their prefix from one place\n(`src/config/adapter-config.ts`), appearing as `spechy_compile_context` etc.\n9 tools, all read-only against canonical knowledge:\n\n| Tool | One-liner |\n|---|---|\n| `compile_context` | The main event — compile the rules for a set of target files |\n| `verify_done` | Mechanically check a diff against `verify`-block constraints |\n| `impact` | Which approved documents do these files map to, and via which edges |\n| `search_logic_flow` | Shortest call path between two code symbols |\n| `get_compile_audit` | Full audit record for a past `compile_id` |\n| `recall` | Episodic index of past runs, plans and session notes |\n| `get_known_tags` | Approved intent-tag catalog + `tag_catalog_hash` for caching |\n| `observe` | Report a gap/decision/outcome — never mutates knowledge itself |\n| `workspace_status` | Read-only dashboard: versions, backlogs, row counts |\n\n### `spechy_compile_context`\n\n| Param | Type | Notes |\n|---|---|---|\n| `target_files` | `string[]` (min 1) | **Required.** Repo-relative paths about to be touched |\n| `target_layers` | `string[]` | Skip layer classification, use these directly |\n| `command` | `string` | Feeds `command_requires`; `\"scaffold\"` also unlocks templates |\n| `plan` | `string` | Free text; enables relevance scoring |\n| `min_relevance` | `0..1` | Drops documents below the threshold (needs `plan`) |\n| `intent_tags` | `string[]` | Cross-cutting tags (e.g. `\"auth\"`) resolved via `tag_mappings` into an additive `expanded` section; `[]` opts out |\n| `max_inline_bytes` | `int > 0` | Inline budget, default `8192` |\n| `content_mode` | `auto \\| always \\| metadata` | Default `auto` — see [Delivery budget](#delivery-budget) |\n| `include_debug` | `boolean` | Adds `debug_info`: near-miss edges, layer classification, budget drops |\n| `agent_id` | `string` | Recorded in the audit log |\n\nResponse: `compile_id`, `snapshot_id`, `knowledge_version`,\n`base.documents[]` (each with `doc_id`, `title`, `kind`, `delivery`,\n`content_bytes`, `content_hash`, plus `content` when inline, `source_path`\nwhen file-backed, `relevance` when a plan was given, `omit_reason` when\ndropped), `base.templates[]`, `base.resolution_path[]`, optional `expanded`,\n`warnings[]`, `notices[]`.\n\n**`warnings` vs `notices`:** warnings are part of the deterministic result —\nsame input, same version, same warnings. Notices report *time-varying*\noperational state: pending proposals, an observation backlog, a stale\nadapter deploy, a newer bundled-template version, an empty knowledge base,\nand failed/reverted attempts from the last 90 days touching the same files.\nBecause they're time-varying, notices are never written into the audit log.\n\n`debug_info.near_miss_edges` is the one to look at when nothing matched: it\nlists patterns that exist but didn't match, so you can tell a wrong glob\nfrom a wrong path.\n\n### `spechy_verify_done`\n\nTakes `diff` (unified diff text) and/or `changed_files` — at least one.\nChecks the changed files/layers against every approved `constraint`\ndocument carrying a fenced ` ```verify ` YAML block\n(`forbid_import: string[]`, `require_companion: string[]`); documents\nwithout the block are silently skipped. Returns `violations[]`\n(`forbidden_import` / `missing_companion`, each with the trigger file and\nevidence), plus best-effort `affected_tests[]` — a one-hop static-import\nscan combined with a git co-change signal, \"run these first\", never \"only\nrun these\".\n\nResults are cached content-addressed in the database (keyed on input +\n`knowledge_version`), with a small ephemeral `.spechy/last-verify.json`\npointer; the `PreCompact` hook re-injects the last verdict after context\ncompaction so a verified change isn't re-litigated. Inspect/prune with\n`spechy-archon verify-cache --status [--prune-stale]`.\n\n### `spechy_impact`\n\n`{ files: string[] }` → every approved document reachable via\n`path_requires`/`layer_requires` (all kinds, not just constraints), plus\nsecond-order documents through `doc_depends_on` — each with\n`evidence[]` (edge type, id, pattern, matched file) and a\n`via_dependency_chain[]` (empty = direct match). `command_requires` is out\nof scope in v0.\n\n### `spechy_search_logic_flow`\n\n`from_symbol`/`to_symbol` (name or `symbol_id`) + optional `max_depth`\n(default and hard cap 10). BFS over the symbol graph's `calls` edges only —\nimports/type references/extends/implements are not execution steps. Returns\nevery path at the shortest distance (`paths: string[][]`), `depth: null`\nwhen unreachable, and `ambiguous_from`/`ambiguous_to` (BFS doesn't run)\nwhen a name matches multiple symbols. Language coverage:\n\n| Language | Extensions | class | function | method | interface | extends | implements |\n|---|---|---|---|---|---|---|---|\n| TypeScript | `.ts` `.tsx` | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |\n| JavaScript | `.js` `.jsx` `.mjs` `.cjs` | ✅ | ✅ | ✅ | — | — | — |\n| PHP | `.php` | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ (incl. trait `use`) |\n| Python | `.py` | ✅ | ✅ | ✅ | — | ✅ | — |\n| Go | `.go` | ✅ (struct) | ✅ | ✅ (receiver) | ✅ | — (no inheritance) | — (implicit) |\n\nOnly file-local qualified-name matches resolve to a concrete\n`to_symbol_id`; cross-file references stay name-only. The index is built by\n`spechy-archon reindex-symbols` (full-repo scan via `git ls-files`,\nunchanged files skipped by content hash, cross-file edges resolved in one\nbatch pass) — installed as a `SessionStart` hook so it refreshes itself.\n\n### `spechy_observe`\n\nThe agent's one write-shaped tool — it records observations, never\ncanonical knowledge:\n\n| `event_type` | Required payload |\n|---|---|\n| `compile_miss` | `target_files[]`, `review_comment` (+ optional `missing_doc`, `target_doc_id`) |\n| `review_correction` | `target_doc_id`, `proposed_content`, `review_comment` |\n| `pr_merged` | `changed_files[]` (+ optional `pr_title`) |\n| `manual_note` | `note` (+ optional `hints[]`, `abstract`) |\n| `document_import`, `doc_gap_detected` | free-form object |\n\n`compile_miss` answers with a `triage_hint` (\"1 near-miss edge exists for\n`src/api/**` — check whether target_files should match it\").\n`manual_note`/`document_import` payloads are secret-scanned (AWS/PEM/\nGitHub/Slack/OpenAI key patterns + entropy) — a hit warns, never blocks.\n\n### `spechy_recall`\n\nFilters: `files`, `run_id`, `recent_runs` (default 10, max 50), free-text\n`search`, `gaps: true` for accumulated near-miss counts. Returns an\n*index* — pointers, not content; follow a `compile_id` into\n`get_compile_audit` for detail. Search ranks episodic hits by a blended\nscore (½ text, ¼ recency, ¼ graph proximity) and penalizes hits whose\nknowledge has since been superseded. Deliberately never injected into\n`compile_context`. Over-budget results say `truncated: true`.\n\n### The rest\n\n`get_compile_audit(compile_id)` returns the recorded request, resolved doc\nids, delivery stats, budget utilization, drops, near-misses, layer\nclassification and duration — errors are logged too, so a failed compile is\nstill auditable. `get_known_tags` lists the approved intent-tag catalog\nwith a `tag_catalog_hash` worth caching. `workspace_status` reports\n`knowledge_version`, latest snapshot, recent compile regions, unresolved\ncounts, pending proposals and canonical row counts — and writes nothing,\nnot even a compile-log row.\n\n## Tools — admin surface\n\nThe admin surface has all 37 tools: the 9 above plus 28 write-path and\ncuration tools.\n\n**Importing & maintaining documents**\n\n| Tool | Notes |\n|---|---|\n| `import_doc` | Direct import as `approved` — one transaction: content + edges + version bump + snapshot. Warns on >4096 bytes, 2+ `##` headings, missing `edge_hints`, likely secrets. Edges accumulate across re-imports |\n| `analyze_doc` / `analyze_import_batch` | Read-only: split source files into suggested import units (by `##` heading), infer `kind`/`tags`/`edge_hints`, flag overlap with approved docs (and between items, for the batch form) |\n| `execute_import_plan` | Turns a reviewed plan into pending `new_doc`/`add_edge` proposals sharing a `bundle_id`. Atomic — one collision rolls back the whole call |\n| `sync_docs` | Drift check for `file-anchored` documents against their sources (whole-file hash or section/line anchor); opens `update_doc` proposals, `dry_run` previews |\n| `set_doc_tags` | Replaces a document's `tag_mappings` entry. Outside the canonical DAG: no version bump, no snapshot, no approval |\n| `get_document` / `get_edge` | Full row by id regardless of status — for chasing ids surfaced by `doctor` |\n\n**Proposals & observations** — the human-approval pipeline\n\n| Tool | Notes |\n|---|---|\n| `list_proposals` | One `status` per call (`pending` default); each carries computed `secret_scan_warnings` |\n| `get_proposal` | Proposal + `evidence_observation_ids[]`, or `null` |\n| `approve_proposal` | Applies the mutation, bumps `knowledge_version`, writes a snapshot; `modifications` shallow-merge over the payload first |\n| `reject_proposal` | Marks rejected with a comment; never touches knowledge |\n| `preflight_proposal_bundle` | Read-only dry run of a bundle: order, dependency/conflict validation, simulated outcome |\n| `approve_proposal_bundle` | Applies a whole bundle in dependency order as **one** version bump + **one** snapshot; validation failure rolls back everything |\n| `process_observations` | Runs every analyzer over unanalyzed observations → `{ proposed, skipped, errors[] }` |\n| `list_observations` / `archive_observations` | Triage helpers; archiving means \"triaged\", not \"resolved\" |\n| `resolve_conflict` | Persists the keep-both / supersede / cancel answer to a `conflict_candidates` hit |\n| `delete_decision` | Deletes a captured decision (standing rule) directly — soft-delete: deprecates the document (edges cascade, version bump, snapshot), history stays intact. Rejects non-standing documents |\n\n**Init, upgrade & operations**\n\n| Tool | Notes |\n|---|---|\n| `init_detect` / `init_confirm` | Template bootstrap with preview + process-scoped hash (see [Building the knowledge base](#building-the-knowledge-base)) |\n| `check_upgrade` / `apply_upgrade` / `sync_init_manifest` | Template upgrade as pending proposals; approve document-first (edge approval doesn't verify its target exists), then re-baseline the manifest |\n| `deploy_adapters` | Same as the CLI `deploy-adapters` — callable by an agent when notices flag a stale adapter file |\n| `doctor` / `get_stats` | Health scan and row counts + doc-usage stats (`never_delivered` hints at `recall({ gaps: true })` for per-edge reasons) |\n| `review_edge_scopes` / `apply_edge_scopes` | Scope review for `path_requires` edges whose glob matches most of the project. Deciding a rule's true scope is a semantic judgement, so archon asks the connected agent instead of guessing; every glob the agent returns is validated against the real file list, and the outcome is a bundle of `remove_edge` + `add_edge` proposals a human still has to approve (see [ADR 0057](./docs/adr/0057-edge-scope-review.md)) |\n| `maintenance` | Read-only gap-coverage preview of what `process_observations` would keep/drop |\n\nDetailed parameter shapes for the init/upgrade family:\n[`docs/adr/0013-init-and-templates.md`](./docs/adr/0013-init-and-templates.md).\n\n## CLI\n\nAll commands share `--db` / `--project-root`.\n\n```bash\nspechy-archon setup                  # interactive setup/update wizard (agent\n                                     #   registration, init, adapter deploy, repair)\nspechy-archon seed <file>            # load a YAML seed file\nspechy-archon stats                  # row counts at a glance\nspechy-archon doctor                 # full workspace health scan\nspechy-archon export <file>          # JSON backup of the whole database\nspechy-archon import <file>          # restore (fully replaces the DB)\nspechy-archon deploy-adapters        # write adapter files + skills + hooks\n                                     #   [--targets claude,cursor,codex] [--dry-run]\nspechy-archon sync-rules-file        # absorb hand-edits to .spechy/rules.md\n                                     #   (diffed add/update/deprecate, never a wipe)\nspechy-archon sync-rules             # sync the shared rules package into documents\n                                     #   [--check-latest] asks npm for newer versions\n                                     #   (network, fail-open; runs on post-merge)\nspechy-archon reindex-symbols        # full-repo tree-sitter symbol reindex\nspechy-archon graph [<file>]         # interactive HTML view of the knowledge base\n                                     #   (default .spechy/graph.html)\nspechy-archon eval [--replay] [--json]\n                                     # delivery-quality report from the audit log;\n                                     #   --replay re-runs logged requests on today's code\nspechy-archon bench [--full] [--external] [--json]\n                                     # retrieval/DAG/resource benchmark; --full adds\n                                     #   LLM-judge A/B (needs ANTHROPIC_API_KEY);\n                                     #   --external adds 15 real-commit cases,\n                                     #   reported separately from the internal corpus\nspechy-archon embed-docs             # compute/update Ollama embeddings\n                                     #   [--model <name>] [--ollama-url <url>]\nspechy-archon verify-cache --status [--prune-stale]\n                                     # inspect / prune the verify_done cache\nspechy-archon prune-log --older-than <days>\n                                     # fold old audit rows into aggregates, then\n                                     #   delete them — no default on purpose\nspechy-archon maintenance            # gap-coverage preview; --reclaim-observations\n                                     #   [--stale-after-days <n>] re-queues analyzed-\n                                     #   but-never-cited observations (default 1 day)\nspechy-archon webui                  # local browser admin panel (127.0.0.1 only)\n                                     #   [--port <n>] [--no-open]\n```\n\nAn unknown command or flag prints usage and exits 1 instead of silently\nstarting the server. The hook forms (`sync-rules --hook`,\n`verify-cache --hook`, `reindex-symbols --hook`) are installed for you by\n`deploy-adapters` — see [Hooks](#hooks).\n\n## Prompts & resources\n\nThe MCP server also exposes three prompts (visible in Claude Code's `/`\nmenu) and one resource:\n\n| Prompt | Args | What it does |\n|---|---|---|\n| `spechy-review` | `target_files` (comma-separated) | Compile context for the files, then review them against exactly what came back |\n| `spechy-scaffold` | `target_files` | Compile with `command: \"scaffold\"` so template documents are included, then follow them |\n| `spechy-explain` | `target_file` | Read-only: summarize the matched documents for a human, propose nothing |\n\n`spechy://guide/workflow` is a markdown operating guide covering the\nread/write/approve cycle — the same content underlying\n[`docs/USAGE.md`](./docs/USAGE.md).\n\n## Knowledge model\n\n**Documents** — `doc_id`, `title`, `kind` (`guideline` / `pattern` /\n`constraint` / `template` / `reference`), `content`, `content_hash`,\n`status`, `source_path`. `template` is special-cased by the allocator.\n\n**Edges** — how a document becomes reachable:\n\n| `edge_type` | Source | Matching |\n|---|---|---|\n| `path_requires` | glob pattern | `picomatch` against each target file |\n| `layer_requires` | layer name | file → layer via `layer_rules`, or `target_layers` |\n| `command_requires` | command name | exact string equality |\n| `doc_depends_on` | `doc_id` | transitive pull-in; cycles rejected at insert |\n\n**Layer rules** — `path_pattern → layer_name`; most specific match wins per\nfile, unmatched classifies as `null`.\n\n**Specificity** is computed from the pattern, never stored by hand: per `/`\nsegment, `**` adds 0, a `*`-containing segment adds 1, a literal adds 2 —\nso `src/api/client.ts` (6) outranks `src/api/**` (4) outranks `src/**` (2).\nOnly `path_requires` edges have specificity. Final ordering is\n`specificity ↓, priority ↑, doc_id ↑` — no ties left to iteration order.\n\n## Delivery budget\n\nEvery resolved document ends up `inline` (content in the response),\n`deferred` (metadata + `source_path`, the agent reads the file itself) or\n`omitted` (policy):\n\n1. **Templates** are omitted unless `command === \"scaffold\"` or\n   `content_mode === \"always\"`.\n2. **Documents without a `source_path`** exist only in the database — there\n   is nothing on disk to defer to, so they always inline. If their total\n   exceeds `max_inline_bytes`, the compile returns a `budget_exceeded`\n   error naming the offenders instead of silently truncating.\n3. **Everything else** competes for the remaining budget, ordered by class\n   (template → document → expanded), then relevance ↓, priority ↑,\n   `doc_id` ↑. Under `auto`, a file-backed document over 4096 bytes never\n   becomes an inline candidate; `metadata` defers everything; `always`\n   makes every file-backed document a candidate.\n\nRelevance (when a `plan` is given) is the fraction of plan terms found in\nthe document — word-boundary and camelCase-aware, purely lexical. It orders\nand optionally filters; it is not semantic search (that's\n[embeddings](#semantic-embeddings)).\n\n## Determinism\n\n| | |\n|---|---|\n| INV-1 | The read path only sees `status = 'approved'` rows |\n| INV-2 | `doc_depends_on` cannot form a cycle |\n| INV-3 | Snapshots are immutable once written |\n| INV-4 | `knowledge_version` increases monotonically |\n| INV-5 | Every compile is auditable (inputs, outputs, snapshot). Two documented narrowings: an unwritable DB reports the missed audit write in `warnings` rather than failing the call, and `prune-log` folds old rows into aggregates before deleting them |\n| INV-6 | The agent surface cannot mutate canonical knowledge — admin tools aren't registered on it at all |\n| P-1 | Same input + same `knowledge_version` = same output |\n| P-3 | Every mutation of canonical knowledge requires human approval |\n\nReasoning behind each: [`docs/INVARIANTS.md`](./docs/INVARIANTS.md) and\n[`docs/adr/`](./docs/adr/).\n\n## Semantic embeddings\n\n**On by default, zero configuration, fully local.** The deterministic DAG\nresult never depends on this — embeddings only *add* suggestions for rules\nabout the same topic in different words (a \"billing\" rule surfacing for a\n\"payments\" plan). Runs against a local [Ollama](https://ollama.com) server;\nnothing leaves your machine.\n\nIf Ollama isn't running when needed, archon **starts it itself and shuts it\ndown after** — it never touches an instance it didn't start. Startup gets up\nto 30 seconds; past that (or with Ollama not installed at all) the call\nfalls back to the plain deterministic result with a note in `warnings`. No\nrequest ever fails because of embeddings.\n\nTo get value from it:\n\n```bash\nollama pull granite-embedding:278m     # once, ~560MB, multilingual\nspechy-archon embed-docs               # re-run after editing rules;\n                                       # only re-embeds what changed\n```\n\n`SPECHY_EMBED_MODEL` and `SPECHY_OLLAMA_URL` customize *which* model/server\n— they don't turn the feature on or off.\n\n## Code awareness\n\nThree layers, all read-only and fail-open:\n\n- **Symbol graph** — `reindex-symbols` parses the repo with tree-sitter\n  (TS/JS/PHP/Python/Go) into `symbols`/`symbol_edges`;\n  `search_logic_flow` answers path questions over it.\n- **Impact analysis** — `impact` maps changed files to the rule surface\n  they enter.\n- **Mechanical verification** — `verify_done` enforces machine-checkable\n  constraint rules against a diff and suggests affected tests, with a\n  compaction-surviving result cache.\n\nDetails under [Tools — agent surface](#tools--agent-surface).\n\n## Episodic memory\n\nEvery server run is recorded (files touched, plan, best-effort session id);\nturn outcomes land as `session_note` observations. `recall` queries this\nhistory on demand, and compile notices proactively mark files with recent\nfailed/reverted attempts. History is kept *out* of `compile_context`'s\nresult on purpose — the past is a pointer, not a prompt tax.\n\n## Document discovery\n\nNew doc-like files added to the repo after your initial import don't slip\nthrough: the `SessionStart` hook diffs `git ls-files` against approved\ndocuments *and* pending proposals, announces \"N new document candidates\" at\nsession start, and points at the `spechy-bulk-import` skill. Discovery\nitself proposes nothing — the import still goes through pending proposals\nand human approval (P-3).\n\n## Graph visualization\n\n```bash\nspechy-archon graph            # writes .spechy/graph.html\nspechy-archon graph out.html   # or wherever\n```\n\nOne interactive HTML file: approved documents, every edge type,\nembedding-similarity links, and the pending backlog (proposals/observations)\nas ghost nodes. No server needed; it loads D3 from a CDN, so viewing needs\ninternet. Good for spotting isolated clusters, over-connected hubs, and\nwhere the backlog accumulates.\n\n## Quality tooling\n\n- **`eval`** — delivery-quality report from the audit log: missed and\n  unnecessary deliveries, budget waste; `--replay` re-runs logged requests\n  against their own snapshot with today's code.\n- **`bench`** — labeled retrieval/DAG/resource corpus; `--external` adds 15\n  real-commit cases reported separately (so \"100% on internal fixtures\"\n  can't hide \"60% on real tasks\"); `--full` adds an LLM-judge generation\n  A/B (needs `ANTHROPIC_API_KEY`, skipped without it).\n- **`doctor`** — the health scan, also callable as an admin tool.\n- **`prune-log`** — audit-log retention with the fold-then-delete rule;\n  auto-generated session notes are pruned, hand-written ones kept.\n\n## Editor adapters\n\n`deploy-adapters` writes a managed rule block into the files editors\nactually read, and installs the bundled skills and hooks:\n\n```bash\nspechy-archon deploy-adapters --db <path> --project-root <path> [--targets claude,cursor,codex] [--dry-run]\n```\n\n| Target | Files |\n|---|---|\n| `claude` | `CLAUDE.md` + `.claude/skills/*/SKILL.md` + `.claude/settings.json` hooks + git hooks |\n| `cursor` | `.cursor/rules/spechy-process.mdc` + `.cursor/skills/*/SKILL.md` |\n| `codex` | `AGENTS.md` + `.codex/skills/*/SKILL.md` |\n\n`CLAUDE.md`/`AGENTS.md` get a block wrapped in `<!-- spechy:start -->` /\n`<!-- spechy:end -->` — everything outside it is yours and never touched.\nMissing/duplicated markers error out rather than guessing at a rewrite. The\nCursor file is entirely spechy-owned (`<!-- spechy:managed -->`); an\nexisting file without that marker is treated as hand-written and reported\nas a `conflict` (which exits 0 — a warning, never a blocker).\n\nOn every compile the server re-renders each deployed target with the\nrunning version's config and compares hashes recorded in `adapter_meta`; a\nmismatch (e.g. after upgrading archon) surfaces as a notice. This does\n*not* detect hand-edits after deploy — the check reads `adapter_meta`, not\nthe file (known limitation, see\n[`docs/adr/0012-adapters.md`](./docs/adr/0012-adapters.md)).\n\nThe rule block itself is the entire enforcement mechanism — MUST/NEVER\ninstructions the agent reads every session. There is no technical gate that\n*forces* an agent to compile first.\n\n## Hooks\n\nInstalled by `deploy-adapters` (claude target). All fail-open: an erroring\nhook logs to stderr and exits 0 — never blocks a session, commit or merge.\n\n**Claude Code hooks** (marker-managed entries in `.claude/settings.json`;\nyour own hooks are left alone):\n\n| Event | Command | Purpose |\n|---|---|---|\n| `SessionStart` + `UserPromptSubmit` | `sync-rules --hook` | Absorb `.spechy/rules.md` edits, inject relevant behaviour rules, commit confirmed rule captures — see [Capturing decisions](#capturing-decisions-standing-rules) |\n| `SessionStart` | `reindex-symbols --hook` | Refresh the symbol index + run [document discovery](#document-discovery) |\n| `PreCompact` | `verify-cache --hook` | Re-inject the last `verify_done` verdict after compaction |\n\n**Git hooks** (managed blocks in `.git/hooks/`):\n\n| Hook | Command | Purpose |\n|---|---|---|\n| `pre-commit` | `sync-rules` | Keep shared rules-package content synced into documents |\n| `post-merge` | `sync-rules --check-latest` | Same, plus one fail-open registry check for a newer rules package |\n\n## Agent Skills\n\nThree [Agent Skills](https://agentskills.io) ship in `skills/` and deploy\nwith the adapters:\n\n| Skill | Use when |\n|---|---|\n| `spechy-setup` | Setting up archon in a project, configuring MCP, bootstrapping knowledge |\n| `spechy-bulk-import` | Bulk-importing existing documentation via the analyze pipeline + bundle approval |\n| `spechy-triage` | Triaging observations, reviewing compile misses, maintaining knowledge quality |\n\nSource lives flat (`skills/spechy-setup.md`); deploy rewrites cross-links\nand drops each at `<target>/skills/<name>/SKILL.md` with a\n`<!-- spechy:managed-skill -->` marker — a hand-written file at that path\nwithout the marker is never overwritten, only reported as a `conflict`.\n\n## Status & limitations\n\nEverything documented above is shipped. Known gaps, current as of this\nwriting:\n\n- **`list_proposals` filters one status per call** — no combined query.\n- **`archive_observations` doesn't check evidence** — archiving an\n  observation already cited by a proposal is allowed on purpose\n  (\"triaged\" ≠ \"resolved\").\n- **`apply_upgrade` doesn't finalize itself** — call `sync_init_manifest`\n  after resolving the bundle, or the same upgrade is offered forever.\n- **`intent_tags` resolve nothing until `set_doc_tags` populates\n  `tag_mappings`** — nothing does that automatically; an SLM tagger port\n  exists (`src/core/read/tagger.ts`) but isn't wired in.\n- **Four packaged templates** (Laravel, Next.js, Python, Go). Vite is a\n  recognized signal without a bundled template. Everything else:\n  bulk-import or manual, via `skip_template: true`.\n- **Adapter staleness detection reads `adapter_meta`, not the files** —\n  hand-edits after deploy go unnoticed.\n- **`search_logic_flow` v1 scope** — Python decorators and Go\n  generics/defined non-struct types are not parsed; Go\n  extends/implements are deliberately empty (no inheritance; interface\n  satisfaction is structural).\n\n## Development\n\n```bash\npnpm install\npnpm test          # vitest\npnpm check         # tsc --noEmit && biome check .\npnpm build         # rm -rf dist && tsc -p tsconfig.build.json\n```\n\nRun a local build without publishing:\n\n```bash\nnode dist/main.js --surface admin --db /tmp/archon.db --project-root \"$PWD\"\n```\n\nLayout: `src/core/store` (schema, repository, snapshot, seed, migrations),\n`src/core/read` (compiler, allocator, relevance, embedder, verify, impact,\nsymbol graph), `src/core/memory` (search, recall, eval, bench, prune),\n`src/core/init` (detection, templates, bootstrap/upgrade),\n`src/core/automation` (observation analyzers, secret scan),\n`src/adapters` (editor targets + hooks), `src/mcp` (server, services),\n`src/config/adapter-config.ts` (tool prefix — change it here, never as a\nstring literal).\n\n## License\n\nUnpublished license terms — internal Spechy project.\n","readmeFilename":""}