@open-agent-toolkit/cli 0.3.7 → 0.3.9

package/dist/commands/init/tools/index.d.ts

@@ -13,7 +13,7 @@ import { type InstallBrainstormOptions, type InstallBrainstormResult } from './b
 import { type InstallCoreOptions, type InstallCoreResult } from './core/install-core.js';
 import { type InstallDocsOptions, type InstallDocsResult } from './docs/install-docs.js';
 import { type InstallIdeasOptions, type InstallIdeasResult } from './ideas/install-ideas.js';
-import { type PlanProjectGuidanceInput, planProjectGuidance } from './project-guidance.js';
+import { type AgentsGuidancePlan, type PlanProjectGuidanceInput, planProjectGuidance, type ProjectGuidancePack } from './project-guidance.js';
 import { type InstallProjectManagementOptions, type InstallProjectManagementResult } from './project-management/install-project-management.js';
 import { type InstallResearchOptions, type InstallResearchResult } from './research/install-research.js';
 import { type InstallUtilityOptions, type InstallUtilityResult } from './utility/install-utility.js';
@@ -78,6 +78,23 @@ interface PackScopeChange {
 export declare function formatReconcileSummary(adds: PackScopeChange[], removes: PackScopeChange[]): string;
 export declare function consumeInitToolsRunMetadata(): InitToolsRunMetadata | null;
 export declare function wasInstallSyncHandled(command: Command): boolean;
+export interface RealizedGuidanceState {
+    packs: ProjectGuidancePack[];
+    /** Project skills that belong to no OAT pack, by name. */
+    otherProjectSkills: string[];
+}
+/**
+ * Reads the realized pack placement (and unrelated project skills) the OAT
+ * tools block describes. Read-only: it inventories and scans installed state
+ * and never installs, upgrades, or writes.
+ */
+export declare function loadRealizedGuidanceState(context: CommandContext, projectRoot: string | null, overrides?: Partial<InitToolsDependencies>): Promise<RealizedGuidanceState>;
+/**
+ * Plans and applies the OAT tools guidance block for the packs already
+ * installed, without installing or upgrading anything. `oat init` uses it to
+ * honor `--project-guidance` when guided setup does not run.
+ */
+export declare function applyProjectGuidanceForInstalledPacks(context: CommandContext, projectRoot: string | null, explicitChoice: boolean, overrides?: Partial<InitToolsDependencies>): Promise<AgentsGuidancePlan>;
 export { buildToolPacksSectionBody } from './project-guidance.js';
 export declare function runInitTools(context: CommandContext, dependencies: InitToolsDependencies, explicitProjectGuidance?: boolean): Promise<ToolPack[]>;
 export declare function runInitToolsWithDefaults(context: CommandContext, explicitProjectGuidance?: boolean): Promise<ToolPack[]>;

package/dist/commands/init/tools/index.d.ts.map

@@ -1 +1 @@
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package/dist/commands/init/tools/index.js

@@ -532,7 +532,11 @@ async function applyProjectGuidance(plan, dependencies) {
         }
         return {
             ...plan,
-            action: sectionResult.action === 'created' ? 'create' : 'no-change',
+            action: sectionResult.action === 'created'
+                ? 'create'
+                : sectionResult.action === 'appended'
+                    ? 'appended'
+                    : 'no-change',
             reason: `Accepted project guidance ${sectionResult.action}. Capability placement and PJM adoption were unchanged.`,
         };
     }
@@ -544,6 +548,50 @@ async function applyProjectGuidance(plan, dependencies) {
         };
     }
 }
+async function realizedGuidanceState(context, repoRoot, assetsRoot, dependencies) {
+    const userRoot = dependencies.resolveScopeRoot('user', context.cwd, context.home);
+    const finalPackStates = await loadInstalledPackStates(repoRoot, userRoot, assetsRoot, dependencies);
+    const packs = ALL_TOOL_PACKS.flatMap((pack) => {
+        const scope = finalPackStates[pack].location;
+        return scope === 'not-installed'
+            ? []
+            : [{ pack, scope }];
+    });
+    return {
+        packs,
+        otherProjectSkills: await otherProjectSkillNames(repoRoot, assetsRoot, dependencies),
+    };
+}
+/**
+ * Project skills whose names belong to no bundled pack. Pack membership, not
+ * directory existence, decides what is "other".
+ */
+async function otherProjectSkillNames(repoRoot, assetsRoot, dependencies) {
+    if (!repoRoot)
+        return [];
+    const projectTools = await dependencies.scanTools({
+        scope: 'project',
+        scopeRoot: repoRoot,
+        assetsRoot,
+    });
+    return projectTools
+        .filter(({ type, pack }) => type === 'skill' && pack === 'custom')
+        .map(({ name }) => name)
+        .sort();
+}
+/**
+ * Reads the realized pack placement (and unrelated project skills) the OAT
+ * tools block describes. Read-only: it inventories and scans installed state
+ * and never installs, upgrades, or writes.
+ */
+export async function loadRealizedGuidanceState(context, projectRoot, overrides = {}) {
+    const dependencies = {
+        ...DEFAULT_DEPENDENCIES,
+        ...overrides,
+    };
+    const assetsRoot = await dependencies.resolveAssetsRoot();
+    return realizedGuidanceState(context, projectRoot, assetsRoot, dependencies);
+}
 async function planAndApplyProjectGuidanceAfterInstall(context, assetsRoot, installedProjectRoot, explicitChoice, dependencies) {
     const initialPlan = await dependencies.planProjectGuidance({
         repoRoot: installedProjectRoot,
@@ -557,17 +605,22 @@ async function planAndApplyProjectGuidanceAfterInstall(context, assetsRoot, inst
     try {
         const repoRoot = installedProjectRoot ??
             (await dependencies.resolveProjectRoot(context.cwd));
-        const userRoot = dependencies.resolveScopeRoot('user', context.cwd, context.home);
-        const finalPackStates = await loadInstalledPackStates(repoRoot, userRoot, assetsRoot, dependencies);
-        const realizedPacks = ALL_TOOL_PACKS.flatMap((pack) => {
-            const scope = finalPackStates[pack].location;
-            return scope === 'not-installed'
-                ? []
-                : [{ pack, scope }];
-        });
+        const realized = await realizedGuidanceState(context, repoRoot, assetsRoot, dependencies);
+        if (realized.packs.length === 0) {
+            // An empty block would be a stale placeholder that turns the first real
+            // pack install into a manual patch, so write nothing.
+            return {
+                ...initialPlan,
+                repoRoot,
+                target: join(repoRoot, 'AGENTS.md'),
+                action: 'skipped',
+                reason: 'No OAT tool pack is installed, so there is no OAT tools guidance to write; AGENTS.md was left unchanged. Run `oat tools install <pack> --project-guidance` or `oat init --setup --project-guidance` to install packs with guidance.',
+            };
+        }
         const completePlan = await dependencies.planProjectGuidance({
             repoRoot,
-            packs: realizedPacks,
+            packs: realized.packs,
+            otherProjectSkills: realized.otherProjectSkills,
             explicitChoice: true,
             interactive: false,
             confirmAction: dependencies.confirmAction,
@@ -582,6 +635,19 @@ async function planAndApplyProjectGuidanceAfterInstall(context, assetsRoot, inst
         };
     }
 }
+/**
+ * Plans and applies the OAT tools guidance block for the packs already
+ * installed, without installing or upgrading anything. `oat init` uses it to
+ * honor `--project-guidance` when guided setup does not run.
+ */
+export async function applyProjectGuidanceForInstalledPacks(context, projectRoot, explicitChoice, overrides = {}) {
+    const dependencies = {
+        ...DEFAULT_DEPENDENCIES,
+        ...overrides,
+    };
+    const assetsRoot = await dependencies.resolveAssetsRoot();
+    return planAndApplyProjectGuidanceAfterInstall(context, assetsRoot, projectRoot, explicitChoice, dependencies);
+}
 function initProviderVisibility(syncScopes) {
     if (syncScopes.length === 0)
         return null;
@@ -1022,6 +1088,7 @@ export async function runInitTools(context, dependencies, explicitProjectGuidanc
         const plannedGuidance = await dependencies.planProjectGuidance({
             repoRoot: projectRoot,
             packs: realizedPacks,
+            otherProjectSkills: await otherProjectSkillNames(projectRoot, assetsRoot, dependencies),
             explicitChoice: explicitProjectGuidance,
             interactive: context.interactive,
             confirmAction: dependencies.confirmAction,
@@ -1171,9 +1238,9 @@ function createReconciledPackCommand(pack, dependencies) {
     };
     const base = new Command(pack).description(descriptions[pack]);
     const scopedCommand = pack === 'core' ? base : withScopeOption(base);
-    const packCommand = pack === 'workflows'
-        ? withProjectGuidanceOptions(scopedCommand)
-        : scopedCommand;
+    // Every pack command acts on --project-guidance: the OAT tools block
+    // describes every installed pack, so any pack install can plan it.
+    const packCommand = withProjectGuidanceOptions(scopedCommand);
     return packCommand
         .allowUnknownOption(false)
         .action(async (_options, command) => {
@@ -1182,9 +1249,7 @@ function createReconciledPackCommand(pack, dependencies) {
         let selection = null;
         let providerContexts = [];
         try {
-            const explicitProjectGuidance = pack === 'workflows'
-                ? commandProjectGuidanceChoice(command)
-                : undefined;
+            const explicitProjectGuidance = commandProjectGuidanceChoice(command);
             const assetsRoot = await dependencies.resolveAssetsRoot();
             const explicitScope = command.getOptionValueSourceWithGlobals('scope') === 'cli';
             const requestedScope = context.scope === 'project' || context.scope === 'user'
@@ -1270,7 +1335,9 @@ function createReconciledPackCommand(pack, dependencies) {
             const providerVisibility = initProviderVisibility(results
                 .filter(({ plan }) => plan.operations.length > 0)
                 .map(({ request }) => request.scope));
-            const projectGuidance = pack === 'workflows'
+            // `workflows` offers guidance on every run (prompting when
+            // interactive); other packs plan it only when the flag is given.
+            const projectGuidance = pack === 'workflows' || explicitProjectGuidance !== undefined
                 ? await planAndApplyProjectGuidanceAfterInstall(context, assetsRoot, requests.find(({ scope }) => scope === 'project')?.scopeRoot ??
                     null, explicitProjectGuidance, dependencies)
                 : null;

package/dist/commands/init/tools/project-guidance.d.ts

@@ -1,4 +1,4 @@
-import type { AgentsMdManualPatch } from '../../shared/agents-md.js';
+import { type AgentsMdManualPatch } from '../../shared/agents-md.js';
 import type { PromptContext } from '../../shared/shared.prompts.js';
 import type { PackName } from '../../tools/shared/types.js';
 import type { Command } from 'commander';
@@ -12,7 +12,7 @@ export type ProjectGuidanceChoice = {
     choice: 'not-requested';
     source: 'non-interactive-default';
 };
-export type AgentsGuidanceAction = 'declined' | 'not-requested' | 'create' | 'no-change' | 'manual-required' | 'blocked';
+export type AgentsGuidanceAction = 'declined' | 'not-requested' | 'create' | 'appended' | 'skipped' | 'no-change' | 'manual-required' | 'blocked';
 export interface ProjectGuidancePack {
     pack: PackName;
     scope: 'project' | 'user' | 'both';
@@ -28,7 +28,14 @@ export interface AgentsGuidancePlan {
     choice: ProjectGuidanceChoice;
     manualPatch?: AgentsMdManualPatch;
 }
-export interface PlanProjectGuidanceInput {
+export interface ToolPacksSectionOptions {
+    /**
+     * Project skills that belong to no OAT pack. They are described separately
+     * and never named as pack skills.
+     */
+    otherProjectSkills?: readonly string[];
+}
+export interface PlanProjectGuidanceInput extends ToolPacksSectionOptions {
     repoRoot: string | null;
     packs: readonly ProjectGuidancePack[];
     explicitChoice?: boolean;
@@ -41,7 +48,15 @@ export declare function reportableProjectGuidance(plan: AgentsGuidancePlan): {
     reason: string;
     manualPatch?: AgentsMdManualPatch | undefined;
 };
-export declare function buildToolPacksSectionBody(packs: readonly ProjectGuidancePack[]): string;
+export declare function isProjectGuidanceIncomplete(plan: AgentsGuidancePlan): boolean;
+/** Prints one guidance plan in the human form every guidance surface uses. */
+export declare function reportProjectGuidancePlan(logger: {
+    info: (message: string) => void;
+    warn: (message: string) => void;
+}, plan: AgentsGuidancePlan): void;
+export declare function buildToolPacksSectionBody(packs: readonly ProjectGuidancePack[], options?: ToolPacksSectionOptions): string;
+/** The complete managed `OAT tools` block, markers included. */
+export declare function renderToolPacksManagedBlock(packs: readonly ProjectGuidancePack[], options?: ToolPacksSectionOptions): string;
 export declare function parseProjectGuidanceFlags(args: readonly string[]): boolean | undefined;
 export declare function commandProjectGuidanceChoice(command: Command): boolean | undefined;
 export declare function withProjectGuidanceOptions<TCommand extends Command>(command: TCommand): TCommand;

package/dist/commands/init/tools/project-guidance.d.ts.map

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package/dist/commands/init/tools/project-guidance.js

@@ -1,4 +1,5 @@
 import { join } from 'node:path';
+import { buildAgentsMdManagedBlock, formatAgentsMdGuidanceResult, } from '../../shared/agents-md.js';
 import { CliError } from '../../../errors/index.js';
 export function reportableProjectGuidance(plan) {
     return {
@@ -8,6 +9,30 @@ export function reportableProjectGuidance(plan) {
         ...(plan.manualPatch ? { manualPatch: plan.manualPatch } : {}),
     };
 }
+export function isProjectGuidanceIncomplete(plan) {
+    return plan.action === 'blocked' || plan.action === 'manual-required';
+}
+/** Prints one guidance plan in the human form every guidance surface uses. */
+export function reportProjectGuidancePlan(logger, plan) {
+    const message = `Project guidance: ${plan.action} — ${plan.reason}`;
+    if (plan.action === 'skipped') {
+        logger.warn(message);
+        return;
+    }
+    if (!isProjectGuidanceIncomplete(plan)) {
+        logger.info(message);
+        return;
+    }
+    logger.warn(message);
+    if (plan.manualPatch) {
+        for (const line of formatAgentsMdGuidanceResult({
+            action: 'manual-required',
+            manualPatch: plan.manualPatch,
+        })) {
+            logger.info(line);
+        }
+    }
+}
 const PACK_DESCRIPTIONS = {
     core: 'Diagnostics and documentation (oat-doctor, oat-docs)',
     docs: 'Documentation and instruction governance workflows',
@@ -18,20 +43,34 @@ const PACK_DESCRIPTIONS = {
     research: 'Research, analysis, verification, and synthesis',
     brainstorm: 'Always-on brainstorming entry point with visual companion',
 };
-export function buildToolPacksSectionBody(packs) {
+export function buildToolPacksSectionBody(packs, options = {}) {
+    // Directories are named by pack membership, never by directory existence:
+    // `oat init --scope project` creates an empty `.agents/skills/`, and
+    // unrelated repository skills may live there.
+    const projectPacks = packs.filter((pack) => pack.scope === 'project' || pack.scope === 'both');
     const userPacks = packs.filter((pack) => pack.scope === 'user' || pack.scope === 'both');
+    const hasOtherProjectSkills = (options.otherProjectSkills?.length ?? 0) > 0;
     const hasWorkflows = packs.some((pack) => pack.pack === 'workflows');
-    const lines = [
-        '## Tool Packs',
-        '',
-        '- **Skills directory:** `.agents/skills/`',
-        '- **Discover available skills:** scan `.agents/skills/*/SKILL.md`',
-        '- **Refresh provider views:** `oat sync --scope all`',
-        '- **Update skills to latest versions:** `oat tools update`',
-    ];
+    const lines = ['## Tool Packs', ''];
+    if (projectPacks.length > 0) {
+        lines.push(`- **Project skills directory:** \`.agents/skills/\` (${projectPacks.map(({ pack }) => pack).join(', ')} packs installed at project scope)`);
+    }
     if (userPacks.length > 0) {
-        lines.push(`- **User-scoped skills:** \`~/.agents/skills/\` (${userPacks.map(({ pack }) => pack).join(', ')} packs installed at user scope)`);
+        lines.push(`- **User skills directory:** \`~/.agents/skills/\` (${userPacks.map(({ pack }) => pack).join(', ')} packs installed at user scope)`);
+    }
+    if (hasOtherProjectSkills) {
+        lines.push('- **Other project skills:** `.agents/skills/` also holds repository skills that belong to no OAT pack; they are not OAT pack skills.');
     }
+    const scanTargets = [
+        ...(projectPacks.length > 0 || hasOtherProjectSkills
+            ? ['`.agents/skills/*/SKILL.md`']
+            : []),
+        ...(userPacks.length > 0 ? ['`~/.agents/skills/*/SKILL.md`'] : []),
+    ];
+    if (scanTargets.length > 0) {
+        lines.push(`- **Discover available skills:** scan ${scanTargets.join(' and ')}`);
+    }
+    lines.push('- **Refresh provider views:** `oat sync --scope all`', '- **Update skills to latest versions:** `oat tools update`');
     lines.push('', '### Installed Packs', '');
     for (const { pack, scope } of packs) {
         const suffix = scope === 'user'
@@ -46,6 +85,10 @@ export function buildToolPacksSectionBody(packs) {
     }
     return lines.join('\n');
 }
+/** The complete managed `OAT tools` block, markers included. */
+export function renderToolPacksManagedBlock(packs, options = {}) {
+    return buildAgentsMdManagedBlock('tools', buildToolPacksSectionBody(packs, options));
+}
 export function parseProjectGuidanceFlags(args) {
     const accepted = args.includes('--project-guidance');
     const declined = args.includes('--no-project-guidance');
@@ -67,7 +110,7 @@ export function commandProjectGuidanceChoice(command) {
 }
 export function withProjectGuidanceOptions(command) {
     if (!command.options.some(({ long }) => long === '--project-guidance')) {
-        command.option('--project-guidance', 'Create missing or print manual repository AGENTS.md tool guidance');
+        command.option('--project-guidance', 'Create or append repository AGENTS.md tool guidance, or print a manual patch');
     }
     if (!command.options.some(({ long }) => long === '--no-project-guidance')) {
         command.option('--no-project-guidance', 'Decline repository AGENTS.md tool guidance');
@@ -89,12 +132,12 @@ export async function planProjectGuidance(input) {
         };
     }
     else {
-        const accepted = await input.confirmAction('Create missing or propose manual repository AGENTS.md tool guidance?', { interactive: input.interactive });
+        const accepted = await input.confirmAction('Create or append repository AGENTS.md tool guidance (a different existing block prints a manual patch)?', { interactive: input.interactive });
         choice = accepted
             ? { choice: 'accepted', source: 'prompt' }
             : { choice: 'declined', source: 'prompt' };
     }
-    const body = buildToolPacksSectionBody(input.packs);
+    const body = buildToolPacksSectionBody(input.packs, input);
     if (choice.choice === 'declined') {
         return {
             repoRoot: input.repoRoot,
@@ -115,7 +158,7 @@ export async function planProjectGuidance(input) {
             sectionKey: 'tools',
             body,
             legacySectionAction: 'preserve',
-            reason: 'Project guidance was not requested. Re-run with --project-guidance to create an absent AGENTS.md or print a manual patch for an existing one.',
+            reason: 'Project guidance was not requested. Re-run with --project-guidance to create an absent AGENTS.md, append an absent guidance block to an existing one, or print a manual patch for a different existing block.',
             choice,
         };
     }
@@ -138,7 +181,7 @@ export async function planProjectGuidance(input) {
         sectionKey: 'tools',
         body,
         legacySectionAction: 'remove',
-        reason: 'Project guidance was accepted. An absent AGENTS.md may be created; an existing file requires a manual patch.',
+        reason: 'Project guidance was accepted. An absent AGENTS.md may be created and an absent guidance block appended; a different existing block requires a manual patch.',
         choice,
     };
 }

package/dist/commands/init/tools/workflows/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../src/commands/init/tools/workflows/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAEL,KAAK,cAAc,EACnB,KAAK,aAAa,EACnB,MAAM,sBAAsB,CAAC;AAC9B,OAAO,EACL,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EAIzB,MAAM,4BAA4B,CAAC;AAEpC,OAAO,EAEL,KAAK,aAAa,EACnB,MAAM,iCAAiC,CAAC;AAQzC,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,mCAAmC,CAAC;AAC1E,OAAO,KAAK,EAAY,QAAQ,EAAE,MAAM,8BAA8B,CAAC;AAGvE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAGL,mBAAmB,EAIpB,MAAM,qBAAqB,CAAC;AAC7B,OAAO,EAEL,KAAK,uBAAuB,EAC5B,KAAK,sBAAsB,EAC3B,KAAK,qBAAqB,EAC3B,MAAM,qBAAqB,CAAC;AAM7B,UAAU,8BAA8B;IACtC,mBAAmB,EAAE,CAAC,OAAO,EAAE,aAAa,KAAK,cAAc,CAAC;IAChE,kBAAkB,EAAE,CAAC,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,CAAC;IACrD,gBAAgB,EAAE,CAChB,KAAK,EAAE,qBAAqB,EAC5B,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,KACT,MAAM,CAAC;IACZ,iBAAiB,EAAE,MAAM,OAAO,CAAC,MAAM,CAAC,CAAC;IACzC,gBAAgB,EAAE,CAChB,OAAO,EAAE,uBAAuB,KAC7B,OAAO,CAAC,sBAAsB,CAAC,CAAC;IACrC,aAAa,EAAE,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,aAAa,KAAK,OAAO,CAAC,OAAO,CAAC,CAAC;IACzE,SAAS,EAAE,CAAC,OAAO,EAAE,gBAAgB,KAAK,OAAO,CAAC,QAAQ,EAAE,CAAC,CAAC;IAC9D,mBAAmB,EAAE,OAAO,mBAAmB,CAAC;IAChD,qBAAqB,EAAE,CACrB,QAAQ,EAAE,MAAM,EAChB,GAAG,EAAE,MAAM,EACX,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE,uBAAuB,KAC9B,OAAO,CAAC,mBAAmB,CAAC,CAAC;CACnC;AAoTD,wBAAgB,+BAA+B,CAC7C,SAAS,GAAE,OAAO,CAAC,8BAA8B,CAAM,GACtD,OAAO,CAuBT"}

package/dist/commands/init/tools/workflows/index.js

@@ -70,7 +70,11 @@ async function applyProjectGuidance(plan, dependencies) {
         }
         return {
             ...plan,
-            action: result.action === 'created' ? 'create' : 'no-change',
+            action: result.action === 'created'
+                ? 'create'
+                : result.action === 'appended'
+                    ? 'appended'
+                    : 'no-change',
             reason: `Accepted project guidance ${result.action}. Capability placement and PJM adoption were unchanged.`,
         };
     }

package/dist/commands/instructions/instructions.types.d.ts

@@ -1,16 +1,40 @@
 import type { Dirent, Stats } from 'node:fs';
 import type { CommandContext, GlobalOptions } from '../../app/command-context.js';
-export declare const INSTRUCTION_SYNC_STRATEGIES: readonly ['pointer', 'symlink', 'copy'];
-export type InstructionSyncStrategy = (typeof INSTRUCTION_SYNC_STRATEGIES)[number];
-export type InstructionStatus = 'ok' | 'missing' | 'content_mismatch' | 'stray';
+import type { InstructionSyncStrategy } from '../../config/oat-config.js';
+export { INSTRUCTION_SYNC_STRATEGIES, type InstructionSyncStrategy, } from '../../config/oat-config.js';
+/**
+ * - `managed_shim`: under strategy `none`, a CLAUDE.md in the exact shape OAT
+ *   writes (the `@AGENTS.md` pointer, a symlink to the sibling AGENTS.md, or a
+ *   byte-identical copy). Drift: sync removes it.
+ * - `unmanaged`: under strategy `none`, a CLAUDE.md that is not an exact
+ *   managed shape (hand-written, modified, a symlink elsewhere). Never
+ *   removed, and not drift.
+ */
+export type InstructionStatus = 'ok' | 'missing' | 'content_mismatch' | 'stray' | 'managed_shim' | 'unmanaged';
+export type ManagedShimShape = 'pointer' | 'symlink' | 'copy';
+/**
+ * What the scan observed about a managed shim, so removal can fail closed if
+ * the file changed between planning and deletion. Internal to the sync apply
+ * path; never serialized into the JSON payload.
+ */
+export interface ManagedShimRecord {
+    shape: ManagedShimShape;
+    /** `lstat` identity of the CLAUDE.md itself (the link for a symlink). */
+    dev: number;
+    ino: number;
+    /** The raw `readlink` value, for the symlink shape only. */
+    linkTarget?: string;
+}
 export type InstructionsStatus = 'ok' | 'drift';
 export interface InstructionEntry {
     agentsPath: string | null;
     claudePath: string;
     status: InstructionStatus;
     detail: string;
+    /** Present only for `managed_shim` entries. */
+    managedShim?: ManagedShimRecord;
 }
-export type InstructionActionType = 'create' | 'update' | 'skip';
+export type InstructionActionType = 'create' | 'update' | 'remove' | 'skip';
 export type InstructionActionResult = 'planned' | 'applied' | 'skipped';
 export interface InstructionActionRecord {
     type: InstructionActionType;
@@ -19,19 +43,69 @@ export interface InstructionActionRecord {
     result: InstructionActionResult;
 }
 export type InstructionsMode = 'validate' | 'dry-run' | 'apply';
+/**
+ * A finding that never changes the exit code by itself.
+ *
+ * `claude_md_hides_agents_md`: under strategy `none`, a `CLAUDE.md`,
+ * `.claude/CLAUDE.md`, or `CLAUDE.local.md` that makes Claude Code's default
+ * `agents-md` mode ignore every AGENTS.md in the project while it exists.
+ */
+export interface ClaudeMdHidesAgentsMdWarning {
+    code: 'claude_md_hides_agents_md';
+    /** Repository-relative POSIX path. */
+    path: string;
+    /**
+     * Repository-relative `AGENTS.md` paths whose symlink chain reaches `path`.
+     * When non-empty, removing `path` would break them: replace each link with
+     * the file's content first. Always present, possibly empty.
+     */
+    linkedBy: string[];
+    message: string;
+}
+/**
+ * `claude_md_blocks_shim_removal`: under strategy `none`, removal is all or
+ * nothing. While any `CLAUDE.md`, `.claude/CLAUDE.md`, or `CLAUDE.local.md`
+ * is not an exact OAT shim, sync removes no CLAUDE.md at all; this finding
+ * names those files and the removals held back. Sync reports each held-back
+ * removal as a skipped action, which is what sets its exit code.
+ */
+export interface ClaudeMdBlocksShimRemovalWarning {
+    code: 'claude_md_blocks_shim_removal';
+    /** Repository-relative POSIX paths of the files with their own content. */
+    paths: string[];
+    /** Repository-relative POSIX paths of the CLAUDE.md files kept because of them. */
+    wouldRemove: string[];
+    /**
+     * For each path in `paths`, the repository-relative `AGENTS.md` paths whose
+     * symlink chain reaches it. A non-empty list means that file holds the only
+     * copy of those instructions: replace each link with its content before
+     * removing it, never remove it plainly. Every path in `paths` has a key.
+     */
+    linkedBy: Record<string, string[]>;
+    message: string;
+}
+export type InstructionsWarning = ClaudeMdHidesAgentsMdWarning | ClaudeMdBlocksShimRemovalWarning;
 export interface InstructionsSummary {
     scanned: number;
     ok: number;
     missing: number;
     contentMismatch: number;
     stray: number;
+    managedShim: number;
+    unmanaged: number;
     created: number;
     updated: number;
+    removed: number;
     skipped: number;
 }
 export interface InstructionsJsonPayload {
     mode: InstructionsMode;
     status: InstructionsStatus;
+    /**
+     * The strategy this run applied or checked: `--strategy` when given, else
+     * `instructions.claude.shims`, else the built-in default.
+     */
+    strategy: InstructionSyncStrategy;
     summary: InstructionsSummary;
     entries: InstructionEntry[];
     actions: InstructionActionRecord[];
@@ -71,6 +145,11 @@ export interface InstructionsJsonPayload {
      * exclusion that silently does nothing. Omitted when empty.
      */
     exclusionWarnings?: string[];
+    /**
+     * Structured warnings, the same text written to stderr in human mode.
+     * Omitted when empty, so a clean repository's payload shape is unchanged.
+     */
+    warnings?: InstructionsWarning[];
 }
 /**
  * The resolved exclusion set, split so that intent and effect cannot be
@@ -104,12 +183,30 @@ export interface InstructionsScanDependencies {
     lstat: (path: string) => Promise<Stats>;
     realpath: (path: string) => Promise<string>;
     readFile: (path: string, encoding: 'utf8') => Promise<string>;
+    /** Raw bytes, for the byte-exact managed-shim comparisons. */
+    readFileBytes: (path: string) => Promise<Buffer>;
     readlink: (path: string) => Promise<string>;
     stat: (path: string) => Promise<Stats>;
 }
 export interface InstructionsValidateCommandDependencies {
     buildCommandContext: (options: GlobalOptions) => CommandContext;
     resolveProjectRoot: (cwd: string) => Promise<string>;
+    /**
+     * The repository's configured `instructions.claude.shims`, or
+     * undefined when the key is absent. Sync inherits it from this interface so
+     * both commands resolve the strategy through the same config read.
+     */
+    readConfiguredInstructionSyncStrategy: (repoRoot: string) => Promise<InstructionSyncStrategy | undefined>;
+    /**
+     * Every `CLAUDE.md` and `CLAUDE.local.md` in the repository (absolute
+     * paths), from a read-only walk that ignores the mutation exclusions, each
+     * classified as an exact OAT shim or not.
+     */
+    findLeftoverClaudeFiles: (repoRoot: string) => Promise<Array<{
+        path: string;
+        linkedBy: string[];
+        exactShim: boolean;
+    }>>;
     /**
      * The single exclusion path both commands resolve through. Sync inherits it
      * from this interface rather than resolving its own, so validate can never
@@ -121,6 +218,10 @@ export interface InstructionsValidateCommandDependencies {
 export interface InstructionsSyncCommandDependencies extends InstructionsValidateCommandDependencies {
     lstat: (path: string) => Promise<Stats>;
     readFile: (path: string, encoding: 'utf8') => Promise<string>;
+    /** Raw bytes, for the apply-time managed-shim re-verification. */
+    readFileBytes: (path: string) => Promise<Buffer>;
+    readlink: (path: string) => Promise<string>;
+    realpath: (path: string) => Promise<string>;
     removeFile: (path: string) => Promise<void>;
     symlinkFile: (target: string, path: string) => Promise<void>;
     writeFile: (path: string, content: string, encoding: 'utf8') => Promise<void>;

package/dist/commands/instructions/instructions.types.d.ts.map

@@ -1 +1 @@
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package/dist/commands/instructions/instructions.types.js

@@ -1,5 +1,4 @@
-export const INSTRUCTION_SYNC_STRATEGIES = [
-    'pointer',
-    'symlink',
-    'copy',
-];
+// One list shared with the `instructions.claude.shims` config
+// normalizer and `oat config set`, so the commands can never accept a value
+// the config rejects or the reverse.
+export { INSTRUCTION_SYNC_STRATEGIES, } from '../../config/oat-config.js';