@imix-js/taproot 0.6.0 → 0.8.0

package/dist/core/dor-runner.js.map

@@ -1 +1 @@
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package/dist/core/fs-walker.js

@@ -5,7 +5,7 @@ const MARKER_FILES = {
     'usecase.md': 'behaviour',
     'impl.md': 'impl',
 };
-const DEFAULT_EXCLUDE = new Set(['_brainstorms', 'skills', '.git', 'node_modules', 'dist', 'global-truths']);
+const DEFAULT_EXCLUDE = new Set(['_brainstorms', 'skills', '.git', 'node_modules', 'dist', 'global-truths', 'agent', 'specs']);
 export function walkHierarchy(rootPath, options = {}) {
     const excludeDirs = options.excludeDirs ?? DEFAULT_EXCLUDE;
     return walkDir(rootPath, rootPath, null, 0, excludeDirs);

package/dist/core/fs-walker.js.map

@@ -1 +1 @@
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package/dist/core/paths.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Returns the absolute path to the agent directory.
+ * New layout: <cwd>/taproot/agent/ (if exists)
+ * Old layout: <cwd>/.taproot/ (fallback)
+ */
+export declare function resolveAgentDir(cwd: string): string;

package/dist/core/paths.js

@@ -0,0 +1,12 @@
+import { existsSync } from 'fs';
+import { join } from 'path';
+/**
+ * Returns the absolute path to the agent directory.
+ * New layout: <cwd>/taproot/agent/ (if exists)
+ * Old layout: <cwd>/.taproot/ (fallback)
+ */
+export function resolveAgentDir(cwd) {
+    const newAgent = join(cwd, 'taproot', 'agent');
+    return existsSync(newAgent) ? newAgent : join(cwd, '.taproot');
+}
+//# sourceMappingURL=paths.js.map

package/dist/core/paths.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"paths.js","sourceRoot":"","sources":["../../src/core/paths.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,IAAI,CAAC;AAChC,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AAE5B;;;;GAIG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,EAAE,SAAS,EAAE,OAAO,CAAC,CAAC;IAC/C,OAAO,UAAU,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,UAAU,CAAC,CAAC;AACjE,CAAC"}

package/dist/core/test-cache.js

@@ -173,7 +173,7 @@ export async function runTestsPassingWithCache(options) {
         return {
             passed: false,
             output: result.summary,
-            correction: `tests-passing blocked: test command timed out after ${timeoutSecs}s. Increase testTimeout in .taproot/settings.yaml if needed.`,
+            correction: `tests-passing blocked: test command timed out after ${timeoutSecs}s. Increase testTimeout in taproot/settings.yaml if needed.`,
         };
     }
     return {

package/dist/core/test-cache.js.map

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package/dist/core/version-check.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Compares the installed taproot version against the project's pinned taproot_version
+ * in taproot/settings.yaml. Emits a warning to stderr when they diverge.
+ *
+ * Skipped silently when:
+ *  - taproot/settings.yaml does not exist (not a taproot project)
+ *  - taproot_version key is absent (project pre-dates version pinning)
+ */
+export declare function checkProjectVersion(cwd: string): void;

package/dist/core/version-check.js

@@ -0,0 +1,43 @@
+import { existsSync, readFileSync } from 'fs';
+import { join, dirname, resolve } from 'path';
+import { fileURLToPath } from 'url';
+import { createRequire } from 'module';
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const require = createRequire(import.meta.url);
+function parseSemver(v) {
+    const parts = v.replace(/^v/, '').split('.').map(Number);
+    return [parts[0] ?? 0, parts[1] ?? 0, parts[2] ?? 0];
+}
+/**
+ * Compares the installed taproot version against the project's pinned taproot_version
+ * in taproot/settings.yaml. Emits a warning to stderr when they diverge.
+ *
+ * Skipped silently when:
+ *  - taproot/settings.yaml does not exist (not a taproot project)
+ *  - taproot_version key is absent (project pre-dates version pinning)
+ */
+export function checkProjectVersion(cwd) {
+    const settingsPath = join(cwd, 'taproot', 'settings.yaml');
+    if (!existsSync(settingsPath))
+        return;
+    const content = readFileSync(settingsPath, 'utf-8');
+    const match = content.match(/^taproot_version:\s*['"]?(\d[\d.]*\d)['"]?\s*$/m);
+    if (!match)
+        return;
+    const projectVersion = match[1];
+    const { version: installed } = require(resolve(__dirname, '..', '..', 'package.json'));
+    const [instMaj, instMin] = parseSemver(installed);
+    const [projMaj, projMin] = parseSemver(projectVersion);
+    if (instMaj < projMaj || (instMaj === projMaj && instMin < projMin)) {
+        process.stderr.write(`taproot: project requires ${projectVersion}, installed is ${installed}\n` +
+            `  → run: npm install -g @imix-js/taproot@${projectVersion}\n`);
+    }
+    else if (instMaj > projMaj) {
+        process.stderr.write(`taproot: installed ${installed} is a major version ahead of this project (pinned at ${projectVersion})\n` +
+            `  → run: taproot update  — to sync skills and record the new version\n`);
+    }
+    else if (instMin > projMin) {
+        process.stderr.write(`taproot: installed ${installed}, project at ${projectVersion} — run: taproot update\n`);
+    }
+}
+//# sourceMappingURL=version-check.js.map

package/dist/core/version-check.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"version-check.js","sourceRoot":"","sources":["../../src/core/version-check.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,IAAI,CAAC;AAC9C,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAC;AAC9C,OAAO,EAAE,aAAa,EAAE,MAAM,KAAK,CAAC;AACpC,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAC;AAEvC,MAAM,SAAS,GAAG,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;AAC1D,MAAM,OAAO,GAAG,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAE/C,SAAS,WAAW,CAAC,CAAS;IAC5B,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACzD,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;AACvD,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,mBAAmB,CAAC,GAAW;IAC7C,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,EAAE,SAAS,EAAE,eAAe,CAAC,CAAC;IAC3D,IAAI,CAAC,UAAU,CAAC,YAAY,CAAC;QAAE,OAAO;IAEtC,MAAM,OAAO,GAAG,YAAY,CAAC,YAAY,EAAE,OAAO,CAAC,CAAC;IACpD,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,iDAAiD,CAAC,CAAC;IAC/E,IAAI,CAAC,KAAK;QAAE,OAAO;IAEnB,MAAM,cAAc,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC;IACjC,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC,OAAO,CAAC,SAAS,EAAE,IAAI,EAAE,IAAI,EAAE,cAAc,CAAC,CAAwB,CAAC;IAE9G,MAAM,CAAC,OAAO,EAAE,OAAO,CAAC,GAAG,WAAW,CAAC,SAAS,CAAC,CAAC;IAClD,MAAM,CAAC,OAAO,EAAE,OAAO,CAAC,GAAG,WAAW,CAAC,cAAc,CAAC,CAAC;IAEvD,IAAI,OAAO,GAAG,OAAO,IAAI,CAAC,OAAO,KAAK,OAAO,IAAI,OAAO,GAAG,OAAO,CAAC,EAAE,CAAC;QACpE,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,6BAA6B,cAAc,kBAAkB,SAAS,IAAI;YAC1E,4CAA4C,cAAc,IAAI,CAC/D,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,GAAG,OAAO,EAAE,CAAC;QAC7B,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,sBAAsB,SAAS,wDAAwD,cAAc,KAAK;YAC1G,wEAAwE,CACzE,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,GAAG,OAAO,EAAE,CAAC;QAC7B,OAAO,CAAC,MAAM,CAAC,KAAK,CAClB,sBAAsB,SAAS,gBAAgB,cAAc,0BAA0B,CACxF,CAAC;IACJ,CAAC;AACH,CAAC"}

package/dist/validators/structure-rules.js

@@ -87,7 +87,7 @@ export function checkGlobalTruthsIntent(root) {
             code: 'GLOBAL_TRUTHS_INTENT_CONFLICT',
             message: '`global-truths/` is a taproot-managed truth store — `intent.md` does not belong here. ' +
                 'Remove `global-truths/intent.md` (and any behaviours beneath it) and use truth files + ' +
-                '`check-if-affected-by` entries in `.taproot/settings.yaml` to enforce them instead.',
+                '`check-if-affected-by` entries in `taproot/settings.yaml` to enforce them instead.',
         }];
 }
 export function validateStructure(root, options) {

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

@@ -1 +1 @@
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package/dist/validators/types.d.ts

@@ -28,20 +28,29 @@ export interface Violation {
     code: string;
     message: string;
 }
+export type WhenQualifier = {
+    'source-matches': string;
+};
 export type DodConditionEntry = string | {
     run: string;
     name?: string;
     correction?: string;
+    when?: WhenQualifier;
 } | {
     'document-current': string;
+    when?: WhenQualifier;
 } | {
     'check-if-affected': string;
+    when?: WhenQualifier;
 } | {
     'check-if-affected-by': string;
+    when?: WhenQualifier;
 } | {
     'check': string;
+    when?: WhenQualifier;
 } | {
     'require-discussion-log': boolean;
+    when?: WhenQualifier;
 };
 export interface TaprootConfig {
     version: number;

package/docs/agents.md

@@ -44,7 +44,10 @@ After `taproot init --agent claude --with-skills`, skills are available as `/tr-
 | `/tr-refine` | Update a behaviour spec based on post-implementation learnings |
 | `/tr-promote` | Escalate a finding from implementation or behaviour level up to the intent |
 | `/tr-analyse-change` | Impact analysis before editing an existing artifact — identifies downstream breakage and related behaviours |
-| `/tr-plan` | Surface the next independently-implementable work item from the hierarchy |
+| `/tr-next` | Surface the next independently-implementable work item from the hierarchy |
+| `/tr-plan` | Build a persistent implementation plan (`taproot/plan.md`) from backlog items, hierarchy gaps, or explicit items |
+| `/tr-plan-execute` | Execute items from `taproot/plan.md` — step-by-step, batch, specify (spec+refine only), or implement (implement only) mode |
+| `/tr-plan-analyse` | Analyse `taproot/plan.md` before execution — check readiness, flag ambiguous specs, unresolved dependencies, and missing prerequisites |
 | `/tr-discover` | Reverse-engineer an existing codebase into a taproot hierarchy through structured, interactive discovery |
 | `/tr-grill-me` | Interview you relentlessly about a plan or design — one decision branch at a time, recommended answer first |
 | `/tr-research` | Research a domain or technical subject before speccing — scans local resources, searches the web, optionally grills domain experts |
@@ -52,12 +55,12 @@ 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
 
@@ -161,7 +161,7 @@ Regenerates `taproot/OVERVIEW.md` — a compact hierarchy summary with clickable
 taproot plan [--format tree|json]
 ```
 
-Surfaces unimplemented behaviours as work items, ordered by priority (intents with more coverage are prioritized to reach completion). Useful for sprint planning or for orienting a new contributor. The `/tr-plan` skill provides an AI-driven version with more context.
+Surfaces unimplemented behaviours as work items, ordered by priority (intents with more coverage are prioritized to reach completion). Useful for sprint planning or for orienting a new contributor. The `/tr-next` skill provides an AI-driven version with more context.
 
 ---
 
@@ -170,11 +170,15 @@ Surfaces unimplemented behaviours as work items, ordered by priority (intents wi
 ### `taproot dod`
 
 ```bash
-taproot dod [impl-path] [--dry-run] [--rerun-tests]
+taproot dod [impl-path] [--dry-run] [--rerun-tests] [--stash] [--ignore-dirty]
 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.
+
+**Uncommitted changes pre-check:** When an `impl-path` is provided, `taproot dod` first checks `git status` for files modified or untracked that are not listed in the impl's `## Source Files`. If such files are found, it reports them and exits with a non-zero code before running any conditions. This prevents uncommitted out-of-scope changes from polluting the implementation commit. Options:
+- `--stash` — automatically run `git stash` before running DoD; restores with `git stash pop` manually after
+- `--ignore-dirty` — skip the dirty check and run DoD regardless of working tree state
 
 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 +208,7 @@ 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.
 
@@ -70,9 +70,33 @@ 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. |
 
+### Scoping conditions with `when:`
+
+Any condition can be scoped to run only when the implementation's `## Source Files` list contains a file matching a glob pattern:
+
+```yaml
+definitionOfDone:
+  - check-if-affected-by: skill-architecture/context-engineering
+    when:
+      source-matches: "skills/*.md"
+  - check-if-affected-by: api-design/rest-conventions
+    when:
+      source-matches: "src/api/**/*.ts"
+```
+
+When `taproot dod` runs for an impl:
+
+- If any source file path listed in `## Source Files` matches the glob → the condition runs normally.
+- If no source file matches → the condition is auto-resolved as `not applicable — no source files match \`<glob>\`` without requiring agent work.
+- If the impl has no `## Source Files` section → all scoped conditions are auto-resolved as `not applicable — impl has no ## Source Files section`.
+
+Glob syntax: `*` matches any characters except `/`; `**` matches across directory separators. A malformed `when:` qualifier (any key other than `source-matches`) produces a parse error result for that condition.
+
+The primary use case is conditions that apply only to a specific implementation type — e.g. skill files, API handlers, CLI commands — to avoid repetitive "not applicable" resolutions across all other impls.
+
 You can give any condition a custom name with `name: <label>`, which is used in DoD reports:
 
 ```yaml
@@ -92,7 +116,7 @@ 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 +145,7 @@ 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>
@@ -48,6 +48,38 @@ When the DoD runner encounters this condition, it instructs the agent to:
 
 ---
 
+## Scoped conditions (`when: source-matches:`)
+
+**Problem:** A cross-cutting condition is relevant only to specific implementation types — for example, a skill-file style guide applies only to impls whose `## Source Files` include `skills/*.md`. Without scoping, every other implementation in the project must record a repetitive "not applicable" resolution, adding noise to DoD runs.
+
+**Pattern:** Add a `when: source-matches: "<glob>"` qualifier to any condition in `definitionOfDone` or `definitionOfReady`.
+
+```yaml
+definitionOfDone:
+  - check-if-affected-by: skill-architecture/context-engineering
+    when:
+      source-matches: "skills/*.md"
+  - check-if-affected-by: api-design/rest-conventions
+    when:
+      source-matches: "src/api/**/*.ts"
+```
+
+The glob is matched against the paths listed in the impl's `## Source Files` section:
+- **Match** → condition runs exactly as if no `when:` qualifier were present
+- **No match** → condition is auto-resolved as `not applicable — no source files match \`<glob>\`` with no agent work
+- **No `## Source Files` section** → all scoped conditions auto-resolve as `not applicable — impl has no ## Source Files section`
+
+**When to use it:**
+- The condition only makes sense for a specific implementation type (skill files, API handlers, CLI commands)
+- You have multiple implementation types sharing the same settings.yaml, and most are not affected by the condition
+- The manual "not applicable" resolutions are adding noise without value
+
+**Glob syntax:** `*` matches any characters except `/`; `**` matches across directory separators. Same conventions as `.gitignore`.
+
+**Limitation:** Scoping is based on listed source file paths — it does not read the files themselves. If an impl omits a file from `## Source Files`, that file is not considered for matching.
+
+---
+
 ## Specific file impact tracking (`check-if-affected`)
 
 **Problem:** Certain files need manual review whenever the codebase changes — a docs index, a CLI help text, a skill guide. You want the DoD to prompt the implementer to check them, without making the check fully automated.
@@ -95,11 +127,11 @@ 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 +146,7 @@ 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 +163,7 @@ 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": "0.8.0",
   "description": "AI-driven specs, enforced at commit time. Code without traceability doesn't merge.",
   "type": "module",
   "bin": {