@seanmars/tospec 0.24.0 → 0.26.0

package/dist/core/global-config.js

@@ -2,6 +2,7 @@ import * as fs from 'node:fs';
 import * as path from 'node:path';
 import * as os from 'node:os';
 import { stripBom } from './parsers/requirement-text.js';
+import { findInvalidConfigFields } from './config-schema.js';
 export const GLOBAL_CONFIG_DIR_NAME = 'tospec';
 export const GLOBAL_CONFIG_FILE_NAME = 'config.json';
 export const GLOBAL_DATA_DIR_NAME = 'tospec';
@@ -78,6 +79,21 @@ export function getLegacyConfigDir(options = {}) {
 export function getGlobalConfigPath() {
     return path.join(getGlobalConfigDir(), GLOBAL_CONFIG_FILE_NAME);
 }
+// Once per line per process: init reads the config several times in one run,
+// and the same line repeated reads as several problems. Keyed by the line, not
+// the path, so a file that turns from one kind of invalid into another within
+// a process still reports the new problem.
+const issuedWarnings = new Set();
+function warnOnce(line) {
+    if (issuedWarnings.has(line))
+        return;
+    issuedWarnings.add(line);
+    console.error(line);
+}
+function warnInvalidSettings(configPath, invalid) {
+    const details = invalid.map((entry) => entry.detail).join('; ');
+    warnOnce(`Warning: Invalid settings in ${configPath} (${details}), ignoring the whole file and using defaults`);
+}
 function readConfigFile(configPath) {
     try {
         const content = fs.readFileSync(configPath, 'utf-8');
@@ -90,7 +106,17 @@ function readConfigFile(configPath) {
         // SyntaxError, and spreading either yields an index-keyed object that would
         // be returned as configuration.
         if (typeof parsed !== 'object' || parsed === null || Array.isArray(parsed)) {
-            console.error(`Warning: ${configPath} is not a JSON object, using defaults`);
+            warnOnce(`Warning: ${configPath} is not a JSON object, using defaults`);
+            return { ...DEFAULT_CONFIG };
+        }
+        // The schema `config set` writes through. Without it a hand-edited
+        // `"workflows": "explore"` reached update as a string (`.filter` threw) and
+        // init as seven one-letter workflows. The whole file falls back, as an
+        // unparseable one does: dropping only the bad field would leave `custom`
+        // with no workflows, and the next update would remove every skill.
+        const invalid = findInvalidConfigFields(parsed);
+        if (invalid.length > 0) {
+            warnInvalidSettings(configPath, invalid);
             return { ...DEFAULT_CONFIG };
         }
         // Loaded values win; unknown keys from older versions pass through.
@@ -99,7 +125,7 @@ function readConfigFile(configPath) {
     catch (error) {
         // A missing file is the normal case and says nothing.
         if (error instanceof SyntaxError) {
-            console.error(`Warning: Invalid JSON in ${configPath}, using defaults`);
+            warnOnce(`Warning: Invalid JSON in ${configPath}, using defaults`);
         }
         return { ...DEFAULT_CONFIG };
     }
@@ -131,11 +157,130 @@ function resolveConfigPath(configDir, legacyConfigDir) {
 export function getEffectiveConfigPath() {
     return resolveConfigPath(getGlobalConfigDir(), getLegacyConfigDir());
 }
-/** Merged over the defaults; a missing or invalid file yields the defaults. */
+/**
+ * Merged over the defaults; a missing or invalid file yields the defaults, and
+ * so does a file with any field the schema refuses.
+ */
 export function getGlobalConfig() {
     return loadGlobalConfigFrom(getGlobalConfigDir(), getLegacyConfigDir());
 }
-export function saveGlobalConfig(config) {
+/**
+ * The object the effective file holds, or `{}` when it is missing or
+ * unparseable. Without the defaults, so a caller can tell an explicit value
+ * from a default.
+ */
+export function getStoredGlobalConfigFields() {
+    try {
+        const parsed = JSON.parse(stripBom(fs.readFileSync(getEffectiveConfigPath(), 'utf-8')));
+        if (typeof parsed === 'object' && parsed !== null && !Array.isArray(parsed)) {
+            return parsed;
+        }
+    }
+    catch {
+        // Missing, or unparseable: saveGlobalConfig refuses to write over the latter.
+    }
+    return {};
+}
+/**
+ * The file's settings, without the schema check reads apply: the base for a
+ * read-modify-write. getGlobalConfig() yields bare defaults for a file with one
+ * invalid field, so saving from it would erase every other setting the user
+ * wrote. Without the defaults too: merged in, the first `config set` of any key
+ * saved `profile: "core"` as well, and `config list` then called the default
+ * profile explicit. Reads still merge the defaults, so nothing reads the gap.
+ */
+export function getStoredGlobalConfig() {
+    return getStoredGlobalConfigFields();
+}
+/**
+ * Whether the config file a read lands on exists but cannot be used: invalid
+ * JSON, not a JSON object, or unreadable (EACCES). A missing file is not
+ * unreadable — it is the normal first-run state.
+ */
+export function isGlobalConfigUnreadable() {
+    const configPath = getEffectiveConfigPath();
+    let content;
+    try {
+        content = fs.readFileSync(configPath, 'utf-8');
+    }
+    catch (error) {
+        return error.code !== 'ENOENT';
+    }
+    try {
+        const parsed = JSON.parse(stripBom(content));
+        return typeof parsed !== 'object' || parsed === null || Array.isArray(parsed);
+    }
+    catch {
+        return true;
+    }
+}
+/** Carries the `status[]` diagnostic the CLI's failure path reads. */
+export class GlobalConfigUnreadableError extends Error {
+    diagnostic;
+    constructor(configPath) {
+        const message = `${configPath} cannot be parsed, so tospec refuses to overwrite it: the write would replace every setting in it with defaults.`;
+        super(message);
+        this.name = 'GlobalConfigUnreadableError';
+        this.diagnostic = {
+            severity: 'error',
+            code: 'global_config_unreadable',
+            message,
+            fix: 'Fix the file with "tospec config edit", or replace it with defaults with "tospec config reset --all".',
+        };
+    }
+}
+/**
+ * For a command whose answer comes from the file, not only its write: `config
+ * unset` on a key the defaults lack writes nothing, and would report "was not
+ * set" about a file it could not read.
+ */
+export function assertGlobalConfigReadable() {
+    if (isGlobalConfigUnreadable()) {
+        throw new GlobalConfigUnreadableError(getEffectiveConfigPath());
+    }
+}
+/** Carries the `status[]` diagnostic the CLI's failure path reads. */
+export class GlobalConfigInvalidError extends Error {
+    diagnostic;
+    constructor(configPath, invalid) {
+        const details = invalid.map((entry) => entry.detail).join('; ');
+        const message = `${configPath} has invalid settings (${details}), so reads ignore the whole file and this write would not take effect.`;
+        super(message);
+        this.name = 'GlobalConfigInvalidError';
+        this.diagnostic = {
+            severity: 'error',
+            code: 'global_config_invalid',
+            message,
+            fix: `Repair it first with "tospec config unset ${invalid[0].field}" or "tospec config set ${invalid[0].field}", or fix the file with "tospec config edit".`,
+        };
+    }
+}
+/**
+ * Refuses a write that leaves every invalid field as it was: reads ignore such
+ * a file, so the write would report success and change nothing, which is why
+ * an unparseable file refuses writes too. A write to an invalid field is the
+ * repair and goes through even with another one left; requiring all of them at
+ * once would refuse `set` and `unset` alike when two are bad, each pointing at
+ * the other.
+ */
+export function assertGlobalConfigWritable(touchedKeys) {
+    const invalid = findInvalidConfigFields(getStoredGlobalConfigFields());
+    if (invalid.length === 0)
+        return;
+    if (invalid.some((entry) => touchedKeys.includes(entry.field)))
+        return;
+    throw new GlobalConfigInvalidError(getEffectiveConfigPath(), invalid);
+}
+/**
+ * Refuses to write over a config file that exists but cannot be parsed. Reads
+ * fall back to defaults for such a file, so a read-modify-write (`config set`,
+ * `unset`, `profile`) would otherwise save those defaults and erase the user's
+ * whole file over one stray comma. `overwriteUnreadable` is for
+ * `config reset --all`, the one write whose purpose is to replace the file.
+ */
+export function saveGlobalConfig(config, options = {}) {
+    if (!options.overwriteUnreadable)
+        assertGlobalConfigReadable();
     const configDir = getGlobalConfigDir();
     const configPath = getGlobalConfigPath();
     if (!fs.existsSync(configDir)) {

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package/dist/core/id.d.ts

@@ -6,4 +6,13 @@ export declare const KEBAB_ID_REGEX: RegExp;
 export declare function isKebabId(value: string): boolean;
 /** Human rendering of the grammar, shared so the wording never forks. */
 export declare const KEBAB_ID_DESCRIPTION = "must be kebab-case with lowercase letters, numbers, and single hyphen separators";
+export declare function isUnicodeKebabName(value: string): boolean;
+export declare const UNICODE_KEBAB_NAME_DESCRIPTION = "is not kebab-case (lowercase letters, numbers, and single hyphen separators; letters with no case, such as \u4E2D\u6587, are allowed)";
+/**
+ * Why `name` cannot exist as a directory on every OS, or undefined when it can.
+ * A name created on Linux or macOS that Windows refuses makes the repo fail to
+ * check out there, so the rule is Windows' even when the project never runs on
+ * it. Worded to follow the name in a sentence: `"con" is a reserved ...`.
+ */
+export declare function portableNameFault(name: string): string | undefined;
 //# sourceMappingURL=id.d.ts.map

package/dist/core/id.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"id.d.ts","sourceRoot":"","sources":["../../src/core/id.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,eAAO,MAAM,cAAc,QAAgC,CAAC;AAE5D,wBAAgB,SAAS,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEhD;AAED,yEAAyE;AACzE,eAAO,MAAM,oBAAoB,qFACmD,CAAC"}
+{"version":3,"file":"id.d.ts","sourceRoot":"","sources":["../../src/core/id.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,eAAO,MAAM,cAAc,QAAgC,CAAC;AAE5D,wBAAgB,SAAS,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEhD;AAED,yEAAyE;AACzE,eAAO,MAAM,oBAAoB,qFACmD,CAAC;AAWrF,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,eAAO,MAAM,8BAA8B,0IACoF,CAAC;AAShI;;;;;GAKG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAUlE"}

package/dist/core/id.js

@@ -8,4 +8,41 @@ export function isKebabId(value) {
 }
 /** Human rendering of the grammar, shared so the wording never forks. */
 export const KEBAB_ID_DESCRIPTION = 'must be kebab-case with lowercase letters, numbers, and single hyphen separators';
+/**
+ * Kebab-case for names a user writes in their own language: a capability is
+ * named after a functional area, and `list --specs` already lays out names like
+ * `中文`. Letters with no case (CJK), modifier letters (the `ー` in katakana) and
+ * combining marks count as lowercase; what stays out is the ASCII grammar's
+ * exclusions — uppercase, `_`, whitespace, doubled or edge hyphens.
+ */
+const UNICODE_KEBAB_NAME_REGEX = /^[\p{Ll}\p{Lm}\p{Lo}\p{M}\p{Nd}]+(?:-[\p{Ll}\p{Lm}\p{Lo}\p{M}\p{Nd}]+)*$/u;
+export function isUnicodeKebabName(value) {
+    return UNICODE_KEBAB_NAME_REGEX.test(value);
+}
+export const UNICODE_KEBAB_NAME_DESCRIPTION = 'is not kebab-case (lowercase letters, numbers, and single hyphen separators; letters with no case, such as 中文, are allowed)';
+// Windows refuses these as a file or directory name in any letter case and with
+// any extension (`con.md` is the console too). The superscript digits are in
+// Microsoft's list as well.
+const WINDOWS_RESERVED_NAME_REGEX = /^(?:con|prn|aux|nul|com[1-9¹²³]|lpt[1-9¹²³])(?:\..*)?$/iu;
+// The characters Win32 forbids in a name, plus the control range it also forbids.
+const WINDOWS_FORBIDDEN_CHAR_REGEX = /[<>:"/\\|?*\u0000-\u001f]/u;
+/**
+ * Why `name` cannot exist as a directory on every OS, or undefined when it can.
+ * A name created on Linux or macOS that Windows refuses makes the repo fail to
+ * check out there, so the rule is Windows' even when the project never runs on
+ * it. Worded to follow the name in a sentence: `"con" is a reserved ...`.
+ */
+export function portableNameFault(name) {
+    if (WINDOWS_RESERVED_NAME_REGEX.test(name))
+        return 'is a reserved device name on Windows';
+    const forbidden = WINDOWS_FORBIDDEN_CHAR_REGEX.exec(name);
+    if (forbidden) {
+        const shown = forbidden[0] < ' ' ? `U+${forbidden[0].charCodeAt(0).toString(16).padStart(4, '0').toUpperCase()}` : forbidden[0];
+        return `contains "${shown}", which Windows does not allow in a file name`;
+    }
+    // Win32 strips a trailing dot or space, so `auth.` and `auth` name one directory.
+    if (/[. ]$/u.test(name))
+        return 'ends with a dot or a space, which Windows strips from a file name';
+    return undefined;
+}
 //# sourceMappingURL=id.js.map

package/dist/core/id.js.map

@@ -1 +1 @@
-{"version":3,"file":"id.js","sourceRoot":"","sources":["../../src/core/id.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,MAAM,CAAC,MAAM,cAAc,GAAG,6BAA6B,CAAC;AAE5D,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AACpC,CAAC;AAED,yEAAyE;AACzE,MAAM,CAAC,MAAM,oBAAoB,GAC/B,kFAAkF,CAAC"}
+{"version":3,"file":"id.js","sourceRoot":"","sources":["../../src/core/id.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,MAAM,CAAC,MAAM,cAAc,GAAG,6BAA6B,CAAC;AAE5D,MAAM,UAAU,SAAS,CAAC,KAAa;IACrC,OAAO,cAAc,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AACpC,CAAC;AAED,yEAAyE;AACzE,MAAM,CAAC,MAAM,oBAAoB,GAC/B,kFAAkF,CAAC;AAErF;;;;;;GAMG;AACH,MAAM,wBAAwB,GAAG,2EAA2E,CAAC;AAE7G,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,wBAAwB,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;AAC9C,CAAC;AAED,MAAM,CAAC,MAAM,8BAA8B,GACzC,6HAA6H,CAAC;AAEhI,gFAAgF;AAChF,6EAA6E;AAC7E,4BAA4B;AAC5B,MAAM,2BAA2B,GAAG,0DAA0D,CAAC;AAC/F,kFAAkF;AAClF,MAAM,4BAA4B,GAAG,4BAA4B,CAAC;AAElE;;;;;GAKG;AACH,MAAM,UAAU,iBAAiB,CAAC,IAAY;IAC5C,IAAI,2BAA2B,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,sCAAsC,CAAC;IAC1F,MAAM,SAAS,GAAG,4BAA4B,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC1D,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,KAAK,GAAG,SAAS,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC;QAChI,OAAO,aAAa,KAAK,gDAAgD,CAAC;IAC5E,CAAC;IACD,kFAAkF;IAClF,IAAI,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,mEAAmE,CAAC;IACpG,OAAO,SAAS,CAAC;AACnB,CAAC"}

package/dist/core/init.d.ts

@@ -1,6 +1,7 @@
 /** Sets up tospec Agent Skills for Claude Code and Codex. */
 type InitCommandOptions = {
     tools?: string;
+    /** Accepted for compatibility and ignored: init never asks before overwriting. */
     force?: boolean;
     interactive?: boolean;
     profile?: string;
@@ -11,7 +12,6 @@ type InitCommandOptions = {
 export declare const INIT_FAILURE_PAYLOAD: Record<string, unknown>;
 export declare class InitCommand {
     private readonly toolsArg?;
-    private readonly force;
     private readonly interactiveOption?;
     private readonly profileOverride?;
     private readonly json;
@@ -50,9 +50,16 @@ export declare class InitCommand {
      */
     private createDirectoryStructure;
     private generateSkillsAndCommands;
+    /**
+     * The canonical sweep cannot stop at .agents/: every dependent tool is a copy
+     * of it, so pruning only the canonical side leaves a tool this run did not
+     * select holding skills the profile dropped, and the two directories disagree
+     * until the next `update`. Prune only, never write: the selection still
+     * decides which tools receive content.
+     */
+    private pruneUnselectedTools;
     private createConfig;
     private displaySuccessMessage;
-    private removeLegacyCommands;
 }
 export {};
 //# sourceMappingURL=init.d.ts.map

package/dist/core/init.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/core/init.ts"],"names":[],"mappings":"AAAA,6DAA6D;AAoD7D,KAAK,kBAAkB,GAAG;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,kFAAkF;IAClF,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,wDAAwD;IACxD,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB,CAAC;AAEF,+EAA+E;AAC/E,eAAO,MAAM,oBAAoB,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAA8B,CAAC;AAsCxF,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAS;IACnC,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAC,CAAU;IAC7C,OAAO,CAAC,QAAQ,CAAC,eAAe,CAAC,CAAS;IAC1C,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAU;IAE/B,YAAY,OAAO,GAAE,kBAAuB,EAK3C;IAED;;;OAGG;IACH,OAAO,CAAC,GAAG;IAIX;;;OAGG;IACH,OAAO,CAAC,IAAI;IAQZ,6EAA6E;IAC7E,OAAO,CAAC,QAAQ,CAAC,YAAY,CAA2B;IAElD,OAAO,CAAC,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAoJ/C;YAEa,QAAQ;IAMtB;;;;;;OAMG;IACH,OAAO,CAAC,wBAAwB;IAiBhC,OAAO,CAAC,sBAAsB;IAM9B,OAAO,CAAC,sBAAsB;YAYhB,gBAAgB;IAoG9B,OAAO,CAAC,eAAe;IAyDvB,OAAO,CAAC,aAAa;IAkCrB;;;;OAIG;YACW,wBAAwB;YAcxB,yBAAyB;IAgGvC;;;;;;OAMG;YACW,oBAAoB;YAqCpB,YAAY;IAgB1B,OAAO,CAAC,qBAAqB;CA8F9B"}

package/dist/core/init.js

@@ -1,6 +1,5 @@
 /** Sets up tospec Agent Skills for Claude Code and Codex. */
 import path from 'path';
-import * as fs from 'fs';
 import { createRequire } from 'module';
 import { FileSystemUtils } from '../utils/file-system.js';
 import { ensureDirectoryAnchor, tospecLayoutDirs } from './project-layout.js';
@@ -8,10 +7,10 @@ import { AI_TOOLS, TOSPEC_DIR_NAME, fallbackToolIds, resolveToolSelection, } fro
 import { isInteractive } from '../utils/interactive.js';
 import { serializeConfig } from './config-prompts.js';
 import { copyDir } from '../utils/link.js';
-import { removeLegacySkillDirs, removeUnselectedSkillDirs, removeLegacyToolSkillLayout, getToolsWithSkillsDir, getToolStates, getSkillTemplates, writeSkillDir, findWorkflowReferenceGaps, describeWorkflowReferenceGaps, DASHBOARD_MOD_TOOL_ID, syncDashboardMod, } from './shared/index.js';
+import { removeLegacySkillDirs, removeUnselectedSkillDirs, removeLegacyToolSkillLayout, removeLegacyCommands, getToolsWithSkillsDir, getToolStates, getConfiguredTools, getSkillTemplates, writeSkillDir, findWorkflowReferenceGaps, describeWorkflowReferenceGaps, DASHBOARD_MOD_TOOL_ID, DASHBOARD_MOD_DIR, syncDashboardMod, } from './shared/index.js';
 import { getGlobalConfig } from './global-config.js';
 import { runLegacyUserStateMigration } from './user-state-migration.js';
-import { getProfileWorkflows, ALL_WORKFLOWS } from './profiles.js';
+import { getProfileWorkflows } from './profiles.js';
 import { getAvailableTools } from './available-tools.js';
 import { resolveConfigFileInDir } from './project-config.js';
 import { planWorkflowRules, writeWorkflowRules } from './shared/rules-generation.js';
@@ -26,15 +25,41 @@ function agentsSkillsDirFor(projectPath) {
 }
 /** The `--json` null-shape; mirrors the success payload with `init` nulled. */
 export const INIT_FAILURE_PAYLOAD = { init: null, root: null };
+/**
+ * A failure init can name and advise on. Carries a full `CommandDiagnostic`:
+ * `asStatus` passes one through by `typeof diagnostic.code === 'string'`, where
+ * a bare Error falls back to `init_error` with no `fix`.
+ */
+class InitError extends Error {
+    diagnostic;
+    constructor(code, message, fix, target) {
+        super(message);
+        this.name = 'InitError';
+        this.diagnostic = { severity: 'error', code, message, target, fix };
+    }
+}
+/**
+ * A file (or anything but a directory) where the layout puts a directory makes
+ * `mkdir` fail with a bare `EEXIST`, which names neither the cause nor a next
+ * step. Checked before any prompt or write, so the run stops before asking for
+ * tools it cannot install. Parents precede children in the list, so a file at
+ * `tospec` is reported before a child path under it is ever probed.
+ */
+async function assertLayoutPathsAreDirectories(projectPath, tospecPath) {
+    for (const dir of [tospecPath, ...tospecLayoutDirs(tospecPath)]) {
+        if ((await FileSystemUtils.fileExists(dir)) && !(await FileSystemUtils.directoryExists(dir))) {
+            const relative = path.relative(projectPath, dir).split(path.sep).join('/');
+            throw new InitError('init_layout_path_not_directory', `"${relative}" exists and is not a directory, so init cannot create the tospec layout there.`, `Move or rename "${relative}", then rerun "tospec init".`, dir);
+        }
+    }
+}
 export class InitCommand {
     toolsArg;
-    force;
     interactiveOption;
     profileOverride;
     json;
     constructor(options = {}) {
         this.toolsArg = options.tools;
-        this.force = options.force ?? false;
         this.interactiveOption = options.interactive;
         this.profileOverride = options.profile;
         this.json = options.json ?? false;
@@ -56,7 +81,7 @@ export class InitCommand {
         if (!this.json) {
             console.log(`Warning: ${message}`);
             if (fix)
-                console.log(fix);
+                console.log(`Fix: ${fix}`);
         }
     }
     /** Emitted alongside the success payload; empty means the key is omitted. */
@@ -67,6 +92,7 @@ export class InitCommand {
         const tospecPath = path.join(projectPath, tospecDir);
         // Detect without writing: even the permission probe must follow rule preflight.
         const extendMode = await FileSystemUtils.directoryExists(tospecPath);
+        await assertLayoutPathsAreDirectories(projectPath, tospecPath);
         const detectedTools = getAvailableTools(projectPath);
         const canPrompt = this.canPromptInteractively();
         if (canPrompt) {
@@ -112,12 +138,44 @@ export class InitCommand {
             silent: this.json,
         });
         this.displaySuccessMessage(projectPath, validatedTools, results, configStatus);
+        // A warning, not progress prose: the run deleted from a tool the caller did
+        // not select, and under `--json` the envelope's `created` / `refreshed`
+        // otherwise say nothing about it.
+        if (results.prunedTools.length > 0) {
+            const removed = results.prunedTools.reduce((sum, tool) => sum + tool.removed, 0);
+            const where = results.prunedTools
+                .map((tool) => `${tool.name} (${tool.skillsDir}/skills/, ${tool.removed})`)
+                .join(', ');
+            this.warn('init_removed_deselected_skills', `Removed ${removed} skill director${removed === 1 ? 'y' : 'ies'} the profile '${initProfile}' does not select from tools this run did not set up: ${where}.`, 'To keep those workflows, add them with "tospec config profile", then run "tospec update".');
+        }
         // After every write, so a run that dies in rule preflight never leaves
         // advice about a state it did not reach; before the JSON envelope, or the
         // warning is recorded into a document already on stdout.
         if (hasResidualCodexOutput(projectPath)) {
             this.warn('codex_residue', RESIDUAL_CODEX_NOTICE, RESIDUAL_CODEX_FIX);
         }
+        // A tool that failed is a partial result, not a success: the envelope stays
+        // complete (`failed` names it) and the exit code says part of the run did
+        // not land, per the batch-command contract. Printed `Failed:` alone, a CI
+        // run or an agent reading exit 0 never saw it.
+        const failures = results.failedTools.map((f) => ({
+            severity: 'error',
+            code: 'init_tool_failed',
+            message: `Failed to set up ${f.name}: ${f.error.message}`,
+            target: f.toolId,
+            fix: "Fix the cause, then rerun 'tospec init'.",
+        }));
+        if (failures.length > 0) {
+            process.exitCode = 1;
+            if (!this.json) {
+                for (const failure of failures) {
+                    console.error(`Error: ${failure.message}`);
+                    if (failure.fix)
+                        console.error(`Fix: ${failure.fix}`);
+                }
+            }
+        }
+        const status = [...failures, ...this.jsonWarnings];
         if (this.json) {
             const globalCfg = getGlobalConfig();
             const activeProfile = this.profileOverride ?? globalCfg.profile ?? 'core';
@@ -128,7 +186,9 @@ export class InitCommand {
                     workflows: activeWorkflows,
                     created: results.createdTools.map((t) => ({ tool: t.value, dir: t.skillsDir })),
                     refreshed: results.refreshedTools.map((t) => ({ tool: t.value, dir: t.skillsDir })),
-                    failed: results.failedTools.map((f) => ({ name: f.name, error: f.error.message })),
+                    // Keyed by tool id like `created` / `refreshed`: the display name is
+                    // prose, and an agent matching it against `--tools` ids never could.
+                    failed: results.failedTools.map((f) => ({ tool: f.toolId, error: f.error.message })),
                     // `created` only records that a tool was configured, so this is the
                     // only field saying what was installed, and it must count what
                     // reached a tool directory: `--tools none` writes nothing anywhere.
@@ -137,7 +197,7 @@ export class InitCommand {
                         : 0,
                     config: configStatus,
                 },
-                ...(this.jsonWarnings.length ? { status: this.jsonWarnings } : {}),
+                ...(status.length ? { status } : {}),
             }, { path: projectPath, source: 'explicit' });
         }
     }
@@ -349,6 +409,10 @@ export class InitCommand {
         const profile = this.resolveProfileOverride() ?? globalConfig.profile ?? 'core';
         const workflows = getProfileWorkflows(profile, globalConfig.workflows);
         const skillTemplates = getSkillTemplates(workflows);
+        // Read before any sweep: an install is recognised by the very skill dirs the
+        // sweeps remove, so afterwards a pruned tool would no longer count as one.
+        const selectedIds = new Set(tools.map((tool) => tool.value));
+        const unselectedInstalled = getConfiguredTools(projectPath).filter((id) => !selectedIds.has(id));
         // Canonical files, written once to .agents/. Gated on "any target at all" so
         // `--tools none` writes nothing; dependency expansion guarantees .agents is
         // present whenever anything else is.
@@ -362,9 +426,10 @@ export class InitCommand {
         // on this run writing anything. Gated, `--tools none` would leave a retired
         // skill dir loadable by every agent reading .agents/skills/, and a dropped
         // workflow would come back on the next copy from the canonical directory.
-        await removeLegacySkillDirs(agentsSkillsDir);
-        await removeUnselectedSkillDirs(agentsSkillsDir, workflows);
-        removedCommandCount += await this.removeLegacyCommands(projectPath);
+        const removedCanonical = (await removeLegacySkillDirs(agentsSkillsDir)) +
+            (await removeUnselectedSkillDirs(agentsSkillsDir, workflows));
+        removedCommandCount += await removeLegacyCommands(projectPath);
+        const prunedTools = await this.pruneUnselectedTools(projectPath, unselectedInstalled, workflows, removedCanonical);
         for (const tool of tools) {
             this.say(`Setting up ${tool.name}...`);
             try {
@@ -397,7 +462,7 @@ export class InitCommand {
             }
             catch (error) {
                 this.say(`Failed for ${tool.name}`);
-                failedTools.push({ name: tool.name, error: error });
+                failedTools.push({ toolId: tool.value, name: tool.name, error: error });
             }
         }
         return {
@@ -405,8 +470,47 @@ export class InitCommand {
             refreshedTools,
             failedTools,
             removedCommandCount,
+            prunedTools,
         };
     }
+    /**
+     * The canonical sweep cannot stop at .agents/: every dependent tool is a copy
+     * of it, so pruning only the canonical side leaves a tool this run did not
+     * select holding skills the profile dropped, and the two directories disagree
+     * until the next `update`. Prune only, never write: the selection still
+     * decides which tools receive content.
+     */
+    async pruneUnselectedTools(projectPath, toolIds, workflows, removedCanonical) {
+        const pruned = [];
+        const agentsSkillsDir = path.resolve(agentsSkillsDirFor(projectPath));
+        for (const toolId of toolIds) {
+            const tool = AI_TOOLS.find((t) => t.value === toolId);
+            if (!tool?.skillsDir)
+                continue;
+            const skillsDir = path.join(projectPath, tool.skillsDir, 'skills');
+            let removed;
+            if (path.resolve(skillsDir) === agentsSkillsDir) {
+                // Already swept above; counted here so the report names it.
+                removed = removedCanonical;
+            }
+            else {
+                removed =
+                    (await removeLegacySkillDirs(skillsDir)) +
+                        (await removeUnselectedSkillDirs(skillsDir, workflows));
+                // The mod goes with the last workflow, as a selected tool's sync does;
+                // with workflows left it stays untouched, since refreshing it is a write.
+                if (toolId === DASHBOARD_MOD_TOOL_ID && workflows.length === 0) {
+                    const hadMod = await FileSystemUtils.directoryExists(path.join(skillsDir, DASHBOARD_MOD_DIR));
+                    await syncDashboardMod(skillsDir, TOSPEC_VERSION, false);
+                    if (hadMod)
+                        removed += 1;
+                }
+            }
+            if (removed > 0)
+                pruned.push({ name: tool.name, skillsDir: tool.skillsDir, removed });
+        }
+        return pruned;
+    }
     async createConfig(tospecPath, extendMode) {
         const configPath = path.join(tospecPath, 'config.yaml');
         if (resolveConfigFileInDir(tospecPath)) {
@@ -494,26 +598,5 @@ export class InitCommand {
         }
         this.say();
     }
-    async removeLegacyCommands(projectPath) {
-        let removed = 0;
-        // Every workflow ships as a skill only. Slash commands duplicated each skill
-        // under a second name in the agent's listing, so every location an earlier
-        // version wrote them to is swept.
-        const legacyPaths = [
-            path.join(projectPath, '.agents', 'commands', 'tospec'),
-            path.join(projectPath, '.claude', 'commands', 'tospec'),
-            path.join(projectPath, '.claude', 'commands', 'tosx'),
-            // Cursor support was removed; this stays so stale .cursor command files
-            // are still swept away.
-            ...ALL_WORKFLOWS.map((workflow) => path.join(projectPath, '.cursor', 'commands', `tospec-${workflow}.md`)),
-        ];
-        for (const legacyPath of legacyPaths) {
-            if (fs.existsSync(legacyPath)) {
-                await fs.promises.rm(legacyPath, { recursive: true, force: true });
-                removed++;
-            }
-        }
-        return removed;
-    }
 }
 //# sourceMappingURL=init.js.map