@imix-js/taproot 0.6.0 → 0.7.0

package/dist/validators/structure-rules.js.map

@@ -1 +1 @@
-{"version":3,"file":"structure-rules.js","sourceRoot":"","sources":["../../src/validators/structure-rules.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,EAAE,UAAU,EAAE,MAAM,IAAI,CAAC;AAEhC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AAEnD,MAAM,UAAU,GAAG,0BAA0B,CAAC;AAE9C,MAAM,UAAU,qBAAqB,CAAC,IAAgB;IACpD,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,IAAI,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,mBAAmB;YACzB,OAAO,EAAE,0CAA0C,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;SACjF,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,IAAgB;IAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,EAAE,CAAC;IAC1C,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,qBAAqB;YAC3B,OAAO,EAAE,gBAAgB,IAAI,CAAC,IAAI,gEAAgE;SACnG,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAAgB;IACnD,IAAI,IAAI,CAAC,MAAM,KAAK,WAAW;QAAE,OAAO,EAAE,CAAC;IAC3C,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,EAAE,MAAM,IAAI,IAAI,CAAC;IACjD,IAAI,YAAY,KAAK,QAAQ,IAAI,YAAY,KAAK,WAAW;QAAE,OAAO,EAAE,CAAC;IACzE,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,YAAY,CAAC;YAC/C,IAAI,EAAE,0BAA0B;YAChC,OAAO,EAAE,qBAAqB,IAAI,CAAC,IAAI,qEAAqE,YAAY,KAAK,IAAI,CAAC,CAAC,CAAC,gCAAgC,CAAC,CAAC,CAAC,MAAM,YAAY,UAAU,EAAE;SACtM,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAgB;IAC9C,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM;QAAE,OAAO,EAAE,CAAC;IACtC,IAAI,IAAI,CAAC,MAAM,EAAE,MAAM,KAAK,WAAW;QAAE,OAAO,EAAE,CAAC;IACnD,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,SAAS,CAAC;YAC5C,IAAI,EAAE,qBAAqB;YAC3B,OAAO,EAAE,0BAA0B,IAAI,CAAC,IAAI,0DAA0D,IAAI,CAAC,MAAM,EAAE,MAAM,KAAK,IAAI,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,MAAM,EAAE,MAAM,IAAI,MAAM,UAAU,EAAE;SAC5M,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,IAAgB;IAChD,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACpC,IAAI,IAAI,CAAC,uBAAuB;QAAE,OAAO,EAAE,CAAC;IAC5C,qEAAqE;IACrE,IAAI,IAAI,CAAC,KAAK,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAChC,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,eAAe;YACrB,OAAO,EAAE,WAAW,IAAI,CAAC,IAAI,oEAAoE;SAClG,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAgB;IAC/C,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACpC,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IACxC,6DAA6D;IAC7D,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM;QAAE,OAAO,EAAE,CAAC;IACtC,OAAO,CAAC;YACN,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,cAAc;YACpB,OAAO,EAAE,GAAG,IAAI,CAAC,MAAM,YAAY,IAAI,CAAC,IAAI,wBAAwB;SACrE,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,IAAgB;IACtD,MAAM,sBAAsB,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,eAAe,EAAE,WAAW,CAAC,CAAC;IACrF,IAAI,CAAC,UAAU,CAAC,sBAAsB,CAAC;QAAE,OAAO,EAAE,CAAC;IACnD,OAAO,CAAC;YACN,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,sBAAsB;YAChC,IAAI,EAAE,+BAA+B;YACrC,OAAO,EAAE,wFAAwF;gBAC/F,yFAAyF;gBACzF,qFAAqF;SACxF,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,IAAgB,EAChB,OAA4B;IAE5B,MAAM,UAAU,GAAgB,EAAE,CAAC;IACnC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC;IAEhC,UAAU,CAAC,IAAI,CAAC,GAAG,uBAAuB,CAAC,IAAI,CAAC,CAAC,CAAC;IAElD,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,UAAU,CAAC,IAAI,CAAC,GAAG,qBAAqB,CAAC,IAAI,CAAC,CAAC,CAAC;QAChD,IAAI,IAAI,KAAK,IAAI;YAAE,UAAU,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5D,UAAU,CAAC,IAAI,CAAC,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC;QAC/C,UAAU,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QAC1C,UAAU,CAAC,IAAI,CAAC,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5C,IAAI,OAAO,CAAC,MAAM;YAAE,UAAU,CAAC,IAAI,CAAC,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC;IACjE,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC"}
+{"version":3,"file":"structure-rules.js","sourceRoot":"","sources":["../../src/validators/structure-rules.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAC5B,OAAO,EAAE,UAAU,EAAE,MAAM,IAAI,CAAC;AAEhC,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AAEnD,MAAM,UAAU,GAAG,0BAA0B,CAAC;AAE9C,MAAM,UAAU,qBAAqB,CAAC,IAAgB;IACpD,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,IAAI,CAAC;QAAE,OAAO,EAAE,CAAC;IAC5C,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,mBAAmB;YACzB,OAAO,EAAE,0CAA0C,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;SACjF,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,IAAgB;IAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,EAAE,CAAC;IAC1C,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,qBAAqB;YAC3B,OAAO,EAAE,gBAAgB,IAAI,CAAC,IAAI,gEAAgE;SACnG,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,IAAgB;IACnD,IAAI,IAAI,CAAC,MAAM,KAAK,WAAW;QAAE,OAAO,EAAE,CAAC;IAC3C,MAAM,YAAY,GAAG,IAAI,CAAC,MAAM,EAAE,MAAM,IAAI,IAAI,CAAC;IACjD,IAAI,YAAY,KAAK,QAAQ,IAAI,YAAY,KAAK,WAAW;QAAE,OAAO,EAAE,CAAC;IACzE,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,YAAY,CAAC;YAC/C,IAAI,EAAE,0BAA0B;YAChC,OAAO,EAAE,qBAAqB,IAAI,CAAC,IAAI,qEAAqE,YAAY,KAAK,IAAI,CAAC,CAAC,CAAC,gCAAgC,CAAC,CAAC,CAAC,MAAM,YAAY,UAAU,EAAE;SACtM,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,IAAgB;IAC9C,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM;QAAE,OAAO,EAAE,CAAC;IACtC,IAAI,IAAI,CAAC,MAAM,EAAE,MAAM,KAAK,WAAW;QAAE,OAAO,EAAE,CAAC;IACnD,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,SAAS,CAAC;YAC5C,IAAI,EAAE,qBAAqB;YAC3B,OAAO,EAAE,0BAA0B,IAAI,CAAC,IAAI,0DAA0D,IAAI,CAAC,MAAM,EAAE,MAAM,KAAK,IAAI,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,MAAM,EAAE,MAAM,IAAI,MAAM,UAAU,EAAE;SAC5M,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,IAAgB;IAChD,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACpC,IAAI,IAAI,CAAC,uBAAuB;QAAE,OAAO,EAAE,CAAC;IAC5C,qEAAqE;IACrE,IAAI,IAAI,CAAC,KAAK,KAAK,CAAC;QAAE,OAAO,EAAE,CAAC;IAChC,OAAO,CAAC;YACN,IAAI,EAAE,OAAO;YACb,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,eAAe;YACrB,OAAO,EAAE,WAAW,IAAI,CAAC,IAAI,oEAAoE;SAClG,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAgB;IAC/C,IAAI,IAAI,CAAC,MAAM,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACpC,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO,EAAE,CAAC;IACxC,6DAA6D;IAC7D,IAAI,IAAI,CAAC,MAAM,KAAK,MAAM;QAAE,OAAO,EAAE,CAAC;IACtC,OAAO,CAAC;YACN,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,IAAI,CAAC,YAAY;YAC3B,IAAI,EAAE,cAAc;YACpB,OAAO,EAAE,GAAG,IAAI,CAAC,MAAM,YAAY,IAAI,CAAC,IAAI,wBAAwB;SACrE,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,IAAgB;IACtD,MAAM,sBAAsB,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,eAAe,EAAE,WAAW,CAAC,CAAC;IACrF,IAAI,CAAC,UAAU,CAAC,sBAAsB,CAAC;QAAE,OAAO,EAAE,CAAC;IACnD,OAAO,CAAC;YACN,IAAI,EAAE,SAAS;YACf,QAAQ,EAAE,sBAAsB;YAChC,IAAI,EAAE,+BAA+B;YACrC,OAAO,EAAE,wFAAwF;gBAC/F,yFAAyF;gBACzF,oFAAoF;SACvF,CAAC,CAAC;AACL,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,IAAgB,EAChB,OAA4B;IAE5B,MAAM,UAAU,GAAgB,EAAE,CAAC;IACnC,MAAM,KAAK,GAAG,WAAW,CAAC,IAAI,CAAC,CAAC;IAEhC,UAAU,CAAC,IAAI,CAAC,GAAG,uBAAuB,CAAC,IAAI,CAAC,CAAC,CAAC;IAElD,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,UAAU,CAAC,IAAI,CAAC,GAAG,qBAAqB,CAAC,IAAI,CAAC,CAAC,CAAC;QAChD,IAAI,IAAI,KAAK,IAAI;YAAE,UAAU,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5D,UAAU,CAAC,IAAI,CAAC,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC;QAC/C,UAAU,CAAC,IAAI,CAAC,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC,CAAC;QAC1C,UAAU,CAAC,IAAI,CAAC,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAC,CAAC;QAC5C,IAAI,OAAO,CAAC,MAAM;YAAE,UAAU,CAAC,IAAI,CAAC,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC;IACjE,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC"}

package/docs/agents.md

@@ -52,12 +52,12 @@ After `taproot init --agent claude --with-skills`, skills are available as `/tr-
 
 ### How skills work
 
-Skills are portable markdown files installed to `.taproot/skills/`. They are not IDE plugins or extensions — any agent that can read files can follow a skill. The Claude Code adapter generates `.claude/commands/tr-*.md` files that reference the skills; invoking `/tr-intent` tells Claude to load and follow `skills/intent.md`.
+Skills are portable markdown files installed to `taproot/agent/skills/`. They are not IDE plugins or extensions — any agent that can read files can follow a skill. The Claude Code adapter generates `.claude/commands/tr-*.md` files that reference the skills; invoking `/tr-intent` tells Claude to load and follow `taproot/agent/skills/intent.md`.
 
 This means:
 - Skills work even if the Claude Code extension is updated or changed
 - You can read any skill file to understand exactly what the agent will do
-- You can customise a skill by editing its file in `.taproot/skills/`
+- You can customise a skill by editing its file in `taproot/agent/skills/`
 - Skills stay in sync with Taproot via `taproot update`
 
 ### Updating skills

package/docs/architecture.md

@@ -22,9 +22,9 @@ Architectural decisions, constraints, and patterns for the taproot codebase. Eve
 
 **No global mutable state** — No module-level variables that accumulate state across calls. Functions that need shared state receive it as parameters.
 
-**`taproot/` contains only requirement documents** — Skills, config, and framework files live in `.taproot/`. Never mix framework files into the requirements hierarchy.
+**Unified `taproot/` directory layout** — All taproot content lives under `taproot/`: requirement documents in `taproot/specs/` (or directly under `taproot/` with a custom `root:` setting), agent skills and docs in `taproot/agent/`, and global truths in `taproot/global-truths/`. Settings live at `taproot/settings.yaml`. The `.taproot/` directory is reserved for gitignored runtime scratch only (session state, test result cache, truth-check sessions).
 
-**`taproot/_sessions/` is the scratch space for agent session state** — Skills that persist resumable session data (phase progress, confirmed items, open questions) write to `taproot/_sessions/<skill-name>-status.md`. This folder is not a formal hierarchy document and is excluded from `taproot validate-structure`. Use `_sessions/`, not `_brainstorms/` — the latter implies ideation rather than structured state.
+**`.taproot/` is runtime scratch, not content** — Files written by CLI invocations that should not be committed (session state, `.truth-check-session`, `.test-results/`) go in `.taproot/`. Add `.taproot/` to `.gitignore`. Never place spec documents, skill files, or configuration there.
 
 **Markdown is the schema** — All hierarchy documents (intent.md, usecase.md, impl.md) must be valid CommonMark. No proprietary extensions.
 
@@ -50,4 +50,4 @@ Core modules must not import from commands. Commands may import from core, valid
 
 ## Testing
 
-Integration tests use real temporary directories (`mkdtempSync`) — no mocking the filesystem. Config in tests must be written to `.taproot/settings.yaml` (not `.taproot/settings.yaml`).
+Integration tests use real temporary directories (`mkdtempSync`) — no mocking the filesystem. Config in tests must be written to `taproot/settings.yaml` (matching the layout that `taproot init` now creates).

package/docs/cli.md

@@ -12,7 +12,7 @@ The Taproot CLI handles setup, validation, and reporting. It does not generate c
 taproot init [--with-hooks] [--with-ci github|gitlab] [--with-skills] [--agent claude|cursor|copilot|windsurf|generic|all] [--template webapp|book-authoring|cli-tool] [--force]
 ```
 
-Initializes Taproot in the current directory. Creates `taproot/` and `.taproot/settings.yaml` if they don't exist, then installs whichever integrations you request.
+Initializes Taproot in the current directory. Creates `taproot/` with `specs/`, `global-truths/`, and `agent/` subdirectories; writes `taproot/settings.yaml`. Then installs whichever integrations you request.
 
 When run on an empty project (no `taproot/` directory yet), the command prompts: **"Start from a template? [y/N]"** — entering `y` presents a list of starter hierarchies to choose from.
 
@@ -21,10 +21,10 @@ When run on an empty project (no `taproot/` directory yet), the command prompts:
 | `--with-hooks` | Installs `.git/hooks/pre-commit` running `taproot commithook` |
 | `--with-ci github` | Generates `.github/workflows/taproot.yml` with validate-structure, validate-format, and check-orphans |
 | `--with-ci gitlab` | Generates a `taproot-validate` job in `.gitlab-ci.yml` |
-| `--with-skills` | Copies skill definitions to `.taproot/skills/`. Implied by `--agent claude` — only needed if you want skills without a Claude adapter. |
+| `--with-skills` | Copies skill definitions to `taproot/agent/skills/`. Implied by `--agent claude` — only needed if you want skills without a Claude adapter. |
 | `--agent <name>` | Generates agent adapter files (see [Agent Setup](agents.md)) |
-| `--template <type>` | Skip the prompt and apply a starter template directly (`webapp`, `book-authoring`, or `cli-tool`). Copies the starter's `taproot/` hierarchy and `.taproot/settings.yaml` into the project. |
-| `--force` | When used with `--template`, overwrites an existing `.taproot/settings.yaml` with the template's version. |
+| `--template <type>` | Skip the prompt and apply a starter template directly (`webapp`, `book-authoring`, or `cli-tool`). Copies the starter's `taproot/` hierarchy and `taproot/settings.yaml` into the project. |
+| `--force` | When used with `--template`, overwrites an existing `taproot/settings.yaml` with the template's version. |
 
 Running `taproot init` again on an existing project is safe — it skips files that already exist and reports `exists` for each.
 
@@ -38,7 +38,7 @@ Refreshes installed agent adapters and skills to the current version. Run this a
 
 The update command also:
 - Removes stale artefacts from older Taproot layouts (e.g., the pre-v0.1 `taproot/skills/` directory)
-- Refreshes `.taproot/docs/` with the current taproot documentation (patterns, architecture, security, etc.) so agent skills have up-to-date reference material
+- Refreshes `taproot/agent/docs/` with the current taproot documentation (patterns, architecture, security, etc.) so agent skills have up-to-date reference material
 - Runs a cross-link refresh: adds missing `## Behaviours <!-- taproot-managed -->` sections to `intent.md` files and `## Implementations <!-- taproot-managed -->` sections to `usecase.md` files, then appends any missing child links and prunes any links to non-existent files
 - Migrates old `taproot validate-structure` / `taproot validate-format` pre-commit hooks to the newer `taproot commithook` format
 
@@ -174,7 +174,7 @@ taproot dod [impl-path] [--dry-run] [--rerun-tests]
 taproot dod <impl-path> --resolve <condition> --note "<text>" [--resolve <condition> --note "<text>" ...]
 ```
 
-Runs all configured DoD conditions from `.taproot/settings.yaml` against the specified implementation (or all implementations if no path is given). If all conditions pass and an `impl-path` is provided, marks the impl `complete`, records the results in `## DoD Resolutions`, and automatically advances the parent `usecase.md` state from `specified` to `implemented` if it hasn't been already.
+Runs all configured DoD conditions from `taproot/settings.yaml` against the specified implementation (or all implementations if no path is given). If all conditions pass and an `impl-path` is provided, marks the impl `complete`, records the results in `## DoD Resolutions`, and automatically advances the parent `usecase.md` state from `specified` to `implemented` if it hasn't been already.
 
 Use `--resolve`/`--note` to record agent resolutions for agent-driven conditions (e.g. `document-current`, `check-if-affected`, `check-if-affected-by`). Multiple pairs can be supplied in a single invocation — conditions are paired with notes by position.
 
@@ -204,7 +204,7 @@ The hook uses a three-tier classification, where the implementation tier is dete
 | Source files found in map but `impl.md` NOT staged | **Blocked** — "Stage `impl.md` alongside your source files. No implementation commit should proceed without its traceability record." |
 | No tracked source files, no hierarchy or impl files | No checks; commit proceeds |
 
-The DoR gate prevents committing an implementation record before the behaviour is fully specified. The DoD gate prevents marking an implementation complete without passing the quality checks defined in `.taproot/settings.yaml`.
+The DoR gate prevents committing an implementation record before the behaviour is fully specified. The DoD gate prevents marking an implementation complete without passing the quality checks defined in `taproot/settings.yaml`.
 
 **Truth consistency check:** when hierarchy files are staged and `taproot/global-truths/` exists, the hook validates that a truth-check session marker (`.taproot/.truth-check-session`) is present and matches the current staged content. This marker is written by `taproot truth-sign`, which `/tr-commit` calls after the agent approves the truth check. Committing hierarchy files directly with `git commit` (bypassing `/tr-commit`) will be blocked if applicable truths exist.
 

package/docs/configuration.md

@@ -2,11 +2,11 @@
 
 ## Quick discovery
 
-- **In your project:** `.taproot/CONFIGURATION.md` — installed and refreshed by `taproot update`, documents all `settings.yaml` options with examples and whether each requires re-running `taproot update`
-- **From the CLI:** `taproot --help` includes a footer pointing to `.taproot/settings.yaml` and `.taproot/CONFIGURATION.md`
+- **In your project:** `taproot/agent/CONFIGURATION.md` — installed and refreshed by `taproot update`, documents all `settings.yaml` options with examples and whether each requires re-running `taproot update`
+- **From the CLI:** `taproot --help` includes a footer pointing to `taproot/settings.yaml` and `taproot/agent/CONFIGURATION.md`
 - **Full reference:** this document
 
-## `.taproot/settings.yaml`
+## `taproot/settings.yaml`
 
 Created by `taproot init`. All settings have defaults — you only need to add what you want to override.
 
@@ -70,7 +70,7 @@ The `definitionOfDone` list controls what `taproot dod` checks and what the pre-
 | `document-current: <description>` | Agent-verified: the agent checks whether the described documentation is current and applies updates if needed. |
 | `check-if-affected: <file>` | Agent-verified: the agent reviews whether the given file needed updating as a result of this implementation and applies changes if needed. |
 | `check-if-affected-by: <behaviour-path>` | Agent-verified: the agent reads the referenced behaviour spec and determines whether it applies to this implementation — verifying compliance if it does, recording "not applicable" if it does not. Use for cross-cutting requirements that every implementation of a given type must satisfy (e.g. every new skill must satisfy `human-integration/contextual-next-steps`). |
-| `check: <free-form question>` | Agent-verified: the agent reads the question, reasons whether the answer is yes, no, or not applicable for this specific implementation, and takes any indicated action (e.g. adds an entry to `.taproot/settings.yaml`, documents a new pattern). The two default entries in `.taproot/settings.yaml` cover the most common meta-questions. |
+| `check: <free-form question>` | Agent-verified: the agent reads the question, reasons whether the answer is yes, no, or not applicable for this specific implementation, and takes any indicated action (e.g. adds an entry to `taproot/settings.yaml`, documents a new pattern). The two default entries in `taproot/settings.yaml` cover the most common meta-questions. |
 | `run: <command>` | Custom shell command. Exit 0 = pass, any other exit code = fail. |
 
 You can give any condition a custom name with `name: <label>`, which is used in DoD reports:
@@ -92,7 +92,7 @@ Results are recorded in the `## DoD Resolutions` section of `impl.md`. The secti
 
 ### Built-in cross-cutting DoD conditions
 
-Taproot's own `.taproot/settings.yaml` ships with several `check-if-affected-by` conditions that enforce project-wide quality rules. These serve as reference examples:
+Taproot's own `taproot/settings.yaml` ships with several `check-if-affected-by` conditions that enforce project-wide quality rules. These serve as reference examples:
 
 | Condition | What it enforces |
 |-----------|-----------------|
@@ -121,7 +121,7 @@ autonomous: true   # all sessions in this repo run without confirmation prompts
 - Test failures or hook rejections are recorded in `impl.md` (impl marked `needs-rework`) and the agent stops — the developer returns to a clear failure report
 
 **Three activation mechanisms (in order of scope):**
-1. `autonomous: true` in `.taproot/settings.yaml` — repo-wide, all sessions
+1. `autonomous: true` in `taproot/settings.yaml` — repo-wide, all sessions
 2. `TAPROOT_AUTONOMOUS=1` environment variable — per process invocation
 3. `--autonomous` flag on a skill invocation (e.g. `/tr-implement path/ --autonomous`) — per skill
 

package/docs/patterns.md

@@ -8,10 +8,10 @@ Reusable patterns for extending and enforcing the taproot hierarchy. Each patter
 
 **Problem:** You have an architectural rule that should apply to every implementation — not just a one-time concern, but a standing requirement. Examples: every skill must include a session hygiene signal; every skill that produces output must present a **What's next?** block; every implementation must satisfy a security review checklist. Writing this rule in a README or CLAUDE.md makes it aspirational. You want it enforced automatically, at commit time, for every new implementation.
 
-**Pattern:** Define the rule as a behaviour spec (`usecase.md`), then add a `check-if-affected-by` entry to `.taproot/settings.yaml`.
+**Pattern:** Define the rule as a behaviour spec (`usecase.md`), then add a `check-if-affected-by` entry to `taproot/settings.yaml`.
 
 ```yaml
-# .taproot/settings.yaml
+# taproot/settings.yaml
 definitionOfDone:
   - check-if-affected-by: skill-architecture/context-engineering
 ```
@@ -37,7 +37,7 @@ When the DoD runner encounters this condition, it instructs the agent to:
 **How to add a new cross-cutting constraint:**
 
 1. Write the spec — `/tr-behaviour taproot/<your-intent>/ "<rule>"` — define what compliance looks like, what non-compliance looks like, and how to resolve it
-2. Add to `.taproot/settings.yaml`:
+2. Add to `taproot/settings.yaml`:
    ```yaml
    definitionOfDone:
      - check-if-affected-by: <intent-slug>/<behaviour-slug>
@@ -95,11 +95,11 @@ The agent is asked: "Does this implementation require changes to `<file>`?" If y
 
 **Problem:** You have a one-off question the agent should reason about at DoD (or DoR) time — something too project-specific to warrant a full behaviour spec, but important enough to enforce at every commit. Examples: "should this story be split?", "does this change affect the public API contract?", "is there a simpler approach we haven't considered?".
 
-**Pattern:** Add a `check:` entry to `definitionOfDone` (or `definitionOfReady`) in `.taproot/settings.yaml`.
+**Pattern:** Add a `check:` entry to `definitionOfDone` (or `definitionOfReady`) in `taproot/settings.yaml`.
 
 ```yaml
 definitionOfDone:
-  - check: "does this story introduce a cross-cutting concern that warrants a new check-if-affected-by or check-if-affected entry in .taproot/settings.yaml?"
+  - check: "does this story introduce a cross-cutting concern that warrants a new check-if-affected-by or check-if-affected entry in taproot/settings.yaml?"
   - check: "does this story reveal a reusable pattern worth documenting in docs/patterns.md?"
 ```
 
@@ -114,7 +114,7 @@ The agent reads the question text, reasons whether the answer is yes, no, or not
 
 | Question | Action if yes |
 |---|---|
-| `does this story introduce a cross-cutting concern that warrants a new check-if-affected-by or check-if-affected entry in .taproot/settings.yaml?` | Agent adds the entry to `.taproot/settings.yaml` |
+| `does this story introduce a cross-cutting concern that warrants a new check-if-affected-by or check-if-affected entry in taproot/settings.yaml?` | Agent adds the entry to `taproot/settings.yaml` |
 | `does this story reveal a reusable pattern worth documenting in docs/patterns.md?` | Agent adds a pattern entry to `docs/patterns.md` |
 
 ---
@@ -131,7 +131,7 @@ The agent reads the question text, reasons whether the answer is yes, no, or not
 Before following any steps, check whether autonomous mode is active:
 - `TAPROOT_AUTONOMOUS=1` is set in the environment, **or**
 - `--autonomous` was passed as an argument to this skill invocation, **or**
-- `.taproot/settings.yaml` contains `autonomous: true`
+- `taproot/settings.yaml` contains `autonomous: true`
 
 If any of these is true, **autonomous mode is active** — apply the autonomous notes at each step where they appear. If none is true, autonomous mode is **inactive** — show confirmation prompts as normal.
 ```

package/docs/security.md

@@ -9,9 +9,9 @@ This document describes taproot's security model, applicable threat categories,
 Taproot has two security boundaries that must be explicitly trusted:
 
 **`settings.yaml` — Executable Configuration**
-The `definitionOfDone` and `definitionOfReady` check entries are executed as shell commands via `spawnSync(..., { shell: true })` in `dod-runner.ts` / `dor-runner.ts`. This is an intentional design — equivalent to `package.json` scripts. The trust boundary is: whoever controls `.taproot/settings.yaml` controls what shell commands run during gate evaluation.
+The `definitionOfDone` and `definitionOfReady` check entries are executed as shell commands via `spawnSync(..., { shell: true })` in `dod-runner.ts` / `dor-runner.ts`. This is an intentional design — equivalent to `package.json` scripts. The trust boundary is: whoever controls `taproot/settings.yaml` controls what shell commands run during gate evaluation.
 
-**`.taproot/skills/` — Agent Instructions**
+**`taproot/agent/skills/` — Agent Instructions**
 Skill files (`.md`) are loaded and delivered as instructions to AI agents. Whoever controls skill content controls agent behaviour. A compromised skill file is a direct agent instruction injection vector.
 
 Both boundaries are intentional; neither should be changed. Both must be consciously managed.
@@ -67,14 +67,14 @@ Recommended controls for taproot's own CI and for projects using taproot:
 
 ## Skill Security Guidelines
 
-All skill files (`.taproot/skills/*.md`, `skills/*.md`) must follow these rules:
+All skill files (`taproot/agent/skills/*.md`, `skills/*.md`) must follow these rules:
 
 1. **No shell execution without validation** — do not instruct agents to run shell commands unless the input is validated or the command is fully static
 2. **No hardcoded credentials or tokens** — skill files are committed to version control and distributed via npm; credentials in skills are a public disclosure
 3. **Least-privilege for agent instructions** — request only the permissions and actions the skill genuinely needs; avoid open-ended "do whatever is needed" patterns
 4. **No sensitive data in output** — do not instruct agents to echo or log content from `settings.yaml` commands (raw command strings, exit output)
 
-Every change to a skill file triggers the DoD skill review condition (see `.taproot/settings.yaml`).
+Every change to a skill file triggers the DoD skill review condition (see `taproot/settings.yaml`).
 
 ---
 

package/docs/workflows.md

@@ -144,7 +144,7 @@ After building up several specs, some domain terms and business rules will recur
 /tr-discover-truths
 ```
 
-The skill scans all `intent.md` and `usecase.md` files, identifies recurring terms, business rules, and conventions not yet defined in `taproot/global-truths/`, and presents them as candidates. For each candidate you choose: **promote** (routes to `/tr-ineed` → define-truth), **backlog** (saves to `.taproot/backlog.md` for later), **skip** (reappears next run), or **dismiss** (permanently suppressed).
+The skill scans all `intent.md` and `usecase.md` files, identifies recurring terms, business rules, and conventions not yet defined in `taproot/global-truths/`, and presents them as candidates. For each candidate you choose: **promote** (routes to `/tr-ineed` → define-truth), **backlog** (saves to `taproot/agent/backlog.md` for later), **skip** (reappears next run), or **dismiss** (permanently suppressed).
 
 Truth discovery also runs as a final pass inside `/tr-review-all`, appending a `## Truth Candidates` section to the review report.
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@imix-js/taproot",
-  "version": "0.6.0",
+  "version": "0.7.0",
   "description": "AI-driven specs, enforced at commit time. Code without traceability doesn't merge.",
   "type": "module",
   "bin": {

package/skills/backlog.md

@@ -14,14 +14,14 @@ Capture ideas, findings, and deferred work mid-session with a single command —
 
 1. Detect that an argument was provided.
 2. If the argument is blank or whitespace only: warn *"Nothing to capture — provide a description."* and stop.
-3. Create `.taproot/backlog.md` if absent. Append the item:
+3. Create `taproot/agent/backlog.md` if absent. Append the item:
    `- [YYYY-MM-DD] <idea>` using today's date.
 4. Confirm in one line: *"✓ Captured: <idea>"*
    No follow-up response required from the developer — the session continues.
 
 ### Triage mode (no argument)
 
-1. Read `.taproot/backlog.md`.
+1. Read `taproot/agent/backlog.md`.
    - If absent or contains no standard items: report *"Backlog is empty. Use `/tr-backlog <idea>` to capture something."* and stop.
 
 2. Present all standard items as a numbered list (FIFO order, oldest first):
@@ -36,8 +36,8 @@ Capture ideas, findings, and deferred work mid-session with a single command —
 3. Offer: `D <n>` discard · `P <n>` promote to /tr-ineed · `A <n>` analyze · `done` finish
 
 4. Accept commands one at a time:
-   - **`D <n>`** — remove item n from `.taproot/backlog.md`. Confirm: *"✓ Discarded #n"*. Redisplay the updated numbered list.
-   - **`P <n>` promote to /tr-ineed** — remove item n from `.taproot/backlog.md`. Invoke `/tr-ineed` with the item text. On return, redisplay the updated numbered list.
+   - **`D <n>`** — remove item n from `taproot/agent/backlog.md`. Confirm: *"✓ Discarded #n"*. Redisplay the updated numbered list.
+   - **`P <n>` promote to /tr-ineed** — remove item n from `taproot/agent/backlog.md`. Invoke `/tr-ineed` with the item text. On return, redisplay the updated numbered list.
    - **`A <n>` analyze** — produce a structured analysis of the item:
      - A short description of what the item is or could be (2–4 sentences)
      - A complexity signal: **simple** / **moderate** / **significant**
@@ -46,7 +46,7 @@ Capture ideas, findings, and deferred work mid-session with a single command —
    - **`done`** — end triage. Items not acted on are kept implicitly.
 
 5. After `done`: *"Triage complete — X discarded, Y promoted, Z kept."*
-   If any non-standard lines were skipped: *"Skipped N non-standard line(s) — they remain in `.taproot/backlog.md`."*
+   If any non-standard lines were skipped: *"Skipped N non-standard line(s) — they remain in `taproot/agent/backlog.md`."*
 
    If the developer exits without `done`: unprocessed items remain unchanged. If any actions were taken, show the summary; otherwise continue naturally.
 
@@ -60,7 +60,7 @@ Capture ideas, findings, and deferred work mid-session with a single command —
 
 ## Output
 
-**Capture:** item written to `.taproot/backlog.md`, one-line confirmation.
+**Capture:** item written to `taproot/agent/backlog.md`, one-line confirmation.
 **Triage:** backlog updated in place; promoted items handed to `/tr-ineed`; completion summary shown.
 
 ## CLI Dependencies
@@ -73,4 +73,4 @@ None.
 - Item format: `- [YYYY-MM-DD] <text>`. Items are presented FIFO (oldest first) during triage.
 - Items promoted via `[P]` are removed from the backlog before `/tr-ineed` is invoked. If the developer abandons the `/tr-ineed` discovery, re-capture the item with `/tr-backlog <idea>`.
 - This is a scratchpad, not a project management tool — no priority, labels, or status tracking.
-- Storage is `.taproot/backlog.md` — a committed markdown file inside the taproot config directory, versioned with the project.
+- Storage is `taproot/agent/backlog.md` — a committed markdown file inside the taproot config directory, versioned with the project.

package/skills/behaviour.md

@@ -15,14 +15,14 @@ Define a UseCase (observable system behaviour) under an intent or another behavi
    - If `parent` contains `intent.md`: read the intent to understand the goal and success criteria.
    - If `parent` contains `usecase.md`: read the parent behaviour — this new behaviour is a sub-behaviour.
 
-1a. **Pattern check** — If `.taproot/docs/patterns.md` exists, scan the behaviour description for semantic matches. Match signals:
+1a. **Pattern check** — If `taproot/agent/docs/patterns.md` exists, scan the behaviour description for semantic matches. Match signals:
    - "apply to all / every implementation / every skill" → `check-if-affected-by`
    - "enforce a rule / architectural constraint / agents should follow" → `check-if-affected-by`
    - "keep docs current / enforce documentation quality" → `document-current`
    - "every new feature must update X" → `check-if-affected: X`
 
    If a match is found, **interrupt before asking clarifying questions**:
-   > "Before I write this spec — that sounds like the **`<pattern-name>`** pattern. <one-line description>. See `.taproot/docs/patterns.md`."
+   > "Before I write this spec — that sounds like the **`<pattern-name>`** pattern. <one-line description>. See `taproot/agent/docs/patterns.md`."
    > **[A] Use this pattern now** — I'll guide you through applying it instead of writing a spec
    > **[B] Continue writing the spec** — the spec is distinct from the pattern
 

package/skills/bug.md

@@ -35,10 +35,10 @@ Diagnose a defect through structured root cause analysis (5-Why) and delegate to
 
    - **No (clearly one-off** — typo, isolated misconfiguration, external incident): note this and continue to step 5.
    - **Yes**: propose prevention across one or more of:
-     - A new DoR or DoD condition to add to `.taproot/settings.yaml`
+     - A new DoR or DoD condition to add to `taproot/settings.yaml`
      - An update to `docs/architecture.md`, `docs/security.md`, or `docs/patterns.md`
 
-   If a satisfactory measure is found: present it — e.g. *"I'll add `check-if-affected-by: <gate>` to `.taproot/settings.yaml`"* or *"I'll add to `docs/security.md`: `<constraint>`"* — and wait for actor confirmation.
+   If a satisfactory measure is found: present it — e.g. *"I'll add `check-if-affected-by: <gate>` to `taproot/settings.yaml`"* or *"I'll add to `docs/security.md`: `<constraint>`"* — and wait for actor confirmation.
    - On **confirm**: apply the change, then continue to step 5.
    - On **reject**: record the recurrence concern in the implicated impl.md `## Notes` and continue to step 5.
 

package/skills/commit.md

@@ -5,7 +5,7 @@
 Before following any steps, check whether autonomous mode is active:
 - `TAPROOT_AUTONOMOUS=1` is set in the environment, **or**
 - `--autonomous` was passed as an argument to this skill invocation, **or**
-- `.taproot/settings.yaml` contains `autonomous: true`
+- `taproot/settings.yaml` contains `autonomous: true`
 
 If any of these is true, **autonomous mode is active** — apply autonomous notes where they appear. If none is true, show confirmation prompts as normal.
 
@@ -35,7 +35,7 @@ Execute the full commit procedure: classify the commit type, run the appropriate
 
    **Autonomous mode:** stage all relevant files and proceed directly without waiting for confirmation.
 
-4. Read `.taproot/settings.yaml` to identify all configured `definitionOfDone` and `definitionOfReady` conditions. If the file does not exist or has no `definitionOfDone`/`definitionOfReady` sections, note: "No user-configured conditions — baseline hook checks only." and proceed to the appropriate sub-flow below.
+4. Read `taproot/settings.yaml` to identify all configured `definitionOfDone` and `definitionOfReady` conditions. If the file does not exist or has no `definitionOfDone`/`definitionOfReady` sections, note: "No user-configured conditions — baseline hook checks only." and proceed to the appropriate sub-flow below.
 
 5. Execute the sub-flow matching the commit type:
 
@@ -78,7 +78,7 @@ Execute the full commit procedure: classify the commit type, run the appropriate
 
 1. Verify parent `usecase.md` is in `specified`, `implemented`, or `complete` state. If it is in `draft` or `proposed` state, report: "Cannot declare implementation — parent `usecase.md` is in `<state>` state. Run `/tr-refine <usecase-path>` to complete the spec first." Stop.
 
-2. Read `.taproot/settings.yaml` `definitionOfReady` entries. For each `check-if-affected-by` or `check:` condition, write an entry directly into `## DoR Resolutions` in the impl.md. There is no `taproot dor` CLI — write entries by hand:
+2. Read `taproot/settings.yaml` `definitionOfReady` entries. For each `check-if-affected-by` or `check:` condition, write an entry directly into `## DoR Resolutions` in the impl.md. There is no `taproot dor` CLI — write entries by hand:
    ```
    condition: <name> | note: <reasoning> | resolved: <date>
    ```

package/skills/discover-truths.md

@@ -13,9 +13,9 @@ Scan the taproot hierarchy for implicit facts — recurring terms, business rule
 Before following any steps, check whether autonomous mode is active:
 - `TAPROOT_AUTONOMOUS=1` is set in the environment, **or**
 - `--autonomous` was passed as an argument to this skill invocation, **or**
-- `.taproot/settings.yaml` contains `autonomous: true`
+- `taproot/settings.yaml` contains `autonomous: true`
 
-If any of these is true, **autonomous mode is active** — skip interactive prompts and defer all candidates to `.taproot/backlog.md` as "truth candidate: `<term>`" entries, then report the summary.
+If any of these is true, **autonomous mode is active** — skip interactive prompts and defer all candidates to `taproot/agent/backlog.md` as "truth candidate: `<term>`" entries, then report the summary.
 
 ## Steps
 
@@ -31,7 +31,7 @@ If any of these is true, **autonomous mode is active** — skip interactive prom
 
 3. Read all files in `taproot/global-truths/` (excluding `intent.md` and subdirectory `usecase.md` files — truth files are files that are NOT named `intent.md` or `usecase.md`). Collect defined terms and rules from them.
 
-4. Read `.taproot/backlog.md` if it exists. Extract all lines matching `reviewed — not a truth: <term>` — these are permanently dismissed candidates. Build a suppression list from them.
+4. Read `taproot/agent/backlog.md` if it exists. Extract all lines matching `reviewed — not a truth: <term>` — these are permanently dismissed candidates. Build a suppression list from them.
 
 ### Phase 3 — Identify Candidates
 
@@ -89,11 +89,11 @@ If any of these is true, **autonomous mode is active** — skip interactive prom
    - No record written; candidate reappears on next discovery run
 
    **Backlog [B]:**
-   - Append to `.taproot/backlog.md`: `- [YYYY-MM-DD] truth candidate: <term>`
+   - Append to `taproot/agent/backlog.md`: `- [YYYY-MM-DD] truth candidate: <term>`
    - Move to next candidate
 
    **Dismiss [D]:**
-   - Append to `.taproot/backlog.md`: `- [YYYY-MM-DD] reviewed — not a truth: <term>`
+   - Append to `taproot/agent/backlog.md`: `- [YYYY-MM-DD] reviewed — not a truth: <term>`
    - This entry suppresses the candidate on all future discovery runs
    - Move to next candidate
 
@@ -113,7 +113,7 @@ If any of these is true, **autonomous mode is active** — skip interactive prom
 ## Output
 
 - Zero or more truth files created in `taproot/global-truths/` (via `/tr-ineed` → define-truth)
-- `.taproot/backlog.md` updated with any backlogged or dismissed candidates
+- `taproot/agent/backlog.md` updated with any backlogged or dismissed candidates
 - Summary report: N promoted, N skipped, N backlogged, N dismissed
 
 ## CLI Dependencies
@@ -125,5 +125,5 @@ None.
 - Truth files in `taproot/global-truths/` are any files that are NOT named `intent.md` or `usecase.md`. They may have any name (e.g. `glossary.md`, `pricing-rules.md`, `entity-model.md`).
 - "Recurring" means 2 or more specs — not just repeated within a single spec.
 - Skip generic language-level words ("the", "a", "is", "not") and taproot structural terms ("intent", "behaviour", "usecase", "implementation") — these are not domain truths.
-- Dismissed entries in `.taproot/backlog.md` are matched by the literal string "reviewed — not a truth: `<term>`" — the suppression logic is substring-match on the candidate term.
+- Dismissed entries in `taproot/agent/backlog.md` are matched by the literal string "reviewed — not a truth: `<term>`" — the suppression logic is substring-match on the candidate term.
 - This skill is read-only on the hierarchy — it never modifies `intent.md` or `usecase.md` files directly.

package/skills/guide.md

@@ -107,7 +107,7 @@ ineed → intent → behaviour → implement → trace → status
    **What's next?**
    [A] `/tr-ineed` — capture your first (or next) requirement
    [B] `/tr-status` — see the current project health at a glance
-   [C] `/tr-backlog` — triage captured ideas (only if `.taproot/backlog.md` is non-empty)
+   [C] `/tr-backlog` — triage captured ideas (only if `taproot/agent/backlog.md` is non-empty)
 
 ## Output
 

package/skills/implement.md

@@ -14,7 +14,7 @@ Implement a behaviour spec: write the code, write the tests, create the `impl.md
 Before following any steps, check whether autonomous mode is active:
 - `TAPROOT_AUTONOMOUS=1` is set in the environment, **or**
 - `--autonomous` was passed as an argument to this skill invocation, **or**
-- `.taproot/settings.yaml` contains `autonomous: true`
+- `taproot/settings.yaml` contains `autonomous: true`
 
 If any of these is true, **autonomous mode is active** — apply the autonomous notes at each step where they appear. If none is true, autonomous mode is **inactive** — show confirmation prompts as normal.
 
@@ -36,14 +36,14 @@ If any of these is true, **autonomous mode is active** — apply the autonomous
    - Read each applicable file; apply defined terms and conventions when choosing the implementation approach, naming, and design decisions
    - If the implementation plan contradicts an applicable truth, surface the conflict before proceeding: "This implementation contradicts `global-truths/<file>`: `<excerpt>`. [A] update plan to align, [B] update the truth, [C] proceed with the conflict noted."
 
-4. **Pattern check + plan mode.** Before proposing the plan: if `.taproot/docs/patterns.md` exists, scan the behaviour description and any design notes for semantic matches. Match signals:
+4. **Pattern check + plan mode.** Before proposing the plan: if `taproot/agent/docs/patterns.md` exists, scan the behaviour description and any design notes for semantic matches. Match signals:
    - "applies to all implementations / cross-cutting concern" → `check-if-affected-by`
    - "enforce a rule on all future work" → `check-if-affected-by`
    - "keep a file in sync / update X on every change" → `check-if-affected: X`
 
    If a match is found, surface it before the plan:
-   > "Before the plan — this looks like it could use the **`<pattern-name>`** pattern rather than a custom implementation. See `.taproot/docs/patterns.md`."
-   > **[A] Use the pattern** — apply it via `.taproot/settings.yaml` instead of writing source code
+   > "Before the plan — this looks like it could use the **`<pattern-name>`** pattern rather than a custom implementation. See `taproot/agent/docs/patterns.md`."
+   > **[A] Use the pattern** — apply it via `taproot/settings.yaml` instead of writing source code
    > **[B] Continue with implementation** — the custom implementation is intentional
 
    Then **propose the implementation plan:**
@@ -102,7 +102,7 @@ If any of these is true, **autonomous mode is active** — apply the autonomous
 6. **Declaration commit** — commit `impl.md`, `discussion.md` (if written), and any `usecase.md` link-section update together (no source files):
 
    Before committing:
-   - Read `.taproot/settings.yaml` and note the `definitionOfReady` conditions — these are the checks the hook will run. If the file has no `definitionOfReady` section, only baseline DoR checks run.
+   - Read `taproot/settings.yaml` and note the `definitionOfReady` conditions — these are the checks the hook will run. If the file has no `definitionOfReady` section, only baseline DoR checks run.
    - There is no standalone `taproot dor` command — DoR runs automatically via the pre-commit hook when impl.md is staged without source files (this is a **declaration commit**). Resolve any agent-driven DoR conditions (e.g. `check-if-affected-by`) in impl.md under `## DoR Resolutions` before staging.
 
    ```

package/skills/ineed.md

@@ -27,7 +27,7 @@ Route a natural language requirement to the right place in the taproot hierarchy
    - **[B]**: proceed to pattern check below.
    - **[C]** or no global truth signal: proceed to pattern check below.
 
-0a. **Pattern check** — If `.taproot/docs/patterns.md` exists, scan the stated requirement for semantic matches against the patterns listed there. Match signals:
+0a. **Pattern check** — If `taproot/agent/docs/patterns.md` exists, scan the stated requirement for semantic matches against the patterns listed there. Match signals:
    - "apply to all / every implementation / every skill / everywhere" → `check-if-affected-by`
    - "guide agents / architecture rules / agents should follow / enforce a rule" → `check-if-affected-by`
    - "enforce documentation / docs must stay current / keep docs accurate" → `document-current`
@@ -35,14 +35,14 @@ Route a natural language requirement to the right place in the taproot hierarchy
    - "research before building / check if a library exists / look up how to implement" → research-first (`/tr-research`)
 
    If a match is found, **interrupt before proceeding**:
-   > "Before I route this — that sounds like the **`<pattern-name>`** pattern. <one-line description>. See `.taproot/docs/patterns.md` for how to use it."
+   > "Before I route this — that sounds like the **`<pattern-name>`** pattern. <one-line description>. See `taproot/agent/docs/patterns.md` for how to use it."
    > **[A] Use this pattern now** — I'll guide you through applying it
    > **[B] Continue as a new requirement** — route and spec it normally
 
-   - **[A]**: read the relevant section of `.taproot/docs/patterns.md` and guide the user through applying the pattern directly. Do not create a new hierarchy entry.
+   - **[A]**: read the relevant section of `taproot/agent/docs/patterns.md` and guide the user through applying the pattern directly. Do not create a new hierarchy entry.
    - **[B]** or no match: proceed to step 1.
 
-   If multiple patterns match, list all before asking. If `.taproot/docs/patterns.md` is absent, skip silently.
+   If multiple patterns match, list all before asking. If `taproot/agent/docs/patterns.md` is absent, skip silently.
 
 1. **Classify the requirement** — Load `taproot/OVERVIEW.md` if it exists; if not, walk `taproot/` and read each `intent.md`. Use this hierarchy map to decide which path to take:
 

package/skills/refine.md

@@ -11,14 +11,14 @@ Update a behaviour spec (`usecase.md`) based on what was learned during or after
 
 ## Steps
 
-0. **Pattern check** — If `.taproot/docs/patterns.md` exists, scan the `finding` input for semantic matches. Match signals:
+0. **Pattern check** — If `taproot/agent/docs/patterns.md` exists, scan the `finding` input for semantic matches. Match signals:
    - "applies to all / every implementation should" → `check-if-affected-by`
    - "enforce a rule / architectural constraint" → `check-if-affected-by`
    - "docs should stay current / keep X updated" → `document-current` or `check-if-affected: X`
 
    If a match is found, **interrupt before reading the spec**:
-   > "Before I refine this — that finding sounds like the **`<pattern-name>`** pattern. <one-line description>. See `.taproot/docs/patterns.md`."
-   > **[A] Apply the pattern** — configure it in `.taproot/settings.yaml` instead of editing the spec
+   > "Before I refine this — that finding sounds like the **`<pattern-name>`** pattern. <one-line description>. See `taproot/agent/docs/patterns.md`."
+   > **[A] Apply the pattern** — configure it in `taproot/settings.yaml` instead of editing the spec
    > **[B] Continue refining** — the spec change is the right approach
 
    - **[A]**: guide through applying the pattern. Do not modify `usecase.md`.

package/skills/review-all.md

@@ -68,7 +68,7 @@ Run a comprehensive review of an entire subtree — an intent and all its descen
 
 8. **Truth discovery pass** — if `taproot/global-truths/` exists and the hierarchy has 3 or more readable `intent.md`/`usecase.md` files (excluding `global-truths/`):
 
-   Run the same scan as `/tr-discover-truths` (Phase 2–3 of that skill): collect candidates not already defined in `global-truths/` and not suppressed by `.taproot/backlog.md` dismissed entries.
+   Run the same scan as `/tr-discover-truths` (Phase 2–3 of that skill): collect candidates not already defined in `global-truths/` and not suppressed by `taproot/agent/backlog.md` dismissed entries.
 
    If candidates are found, append to the report:
 
@@ -86,7 +86,7 @@ Run a comprehensive review of an entire subtree — an intent and all its descen
 
    **If [P]:** invoke `/tr-discover-truths` inline; return here when it completes.
 
-   **If [D]:** append each candidate to `.taproot/backlog.md` as `- [YYYY-MM-DD] truth candidate: <term>`.
+   **If [D]:** append each candidate to `taproot/agent/backlog.md` as `- [YYYY-MM-DD] truth candidate: <term>`.
 
    If no candidates found (hierarchy consistent with existing truths), append to report:
    ```

package/skills/status.md

@@ -78,13 +78,13 @@ Generated: <date>
      [B] `/tr-refine taproot/<intent>/<behaviour>/` — add missing tests
      [C] `/tr-plan` — pick a different next item
 
-   - **If no specific items were found** (healthy project): check whether `.taproot/backlog.md` exists and contains items. Show the generic fallback menu:
+   - **If no specific items were found** (healthy project): check whether `taproot/agent/backlog.md` exists and contains items. Show the generic fallback menu:
 
      **What's next?**
      [A] `/tr-plan` — pick the next behaviour to implement
      [B] `/tr-ineed` — route a new requirement into the hierarchy
      [C] `/tr-review-all` — deeper semantic review of specs
-     [D] `/tr-backlog` — triage captured ideas (only if `.taproot/backlog.md` is non-empty)
+     [D] `/tr-backlog` — triage captured ideas (only if `taproot/agent/backlog.md` is non-empty)
 
 ## Output