fix(#1415): loadConfig provenance + agent-skills diagnostic (Resolution Provenance P2) (#1424)

Implements ADR-1411 P2 / #1415, closing #1366.

Part 1 — config-loader.cts:
- Adds `loadConfigResolved(cwd, options) → ConfigResolution { config, source, degraded }`
  with six tagged branch return paths:
  A1 ws+wsconfig → source:'workstream', degraded:false
  A2 no-ws+config → source:'root', degraded:false
  B  ws requested, wsconfig absent → source:'root', degraded:true (intercepts recursive call)
  C  .planning/ exists, no config → source:'builtin-defaults', degraded:false
  D  no .planning/, global defaults readable → source:'global-defaults', degraded:false
  E  no .planning/, no global → source:'builtin-defaults', degraded:false
- `loadConfigResolved` calls `findProjectRoot` at entry to anchor resolution to the
  nearest .planning/ ancestor (cwd-drift fix, heuristic 4 from P1)
- `loadConfig` becomes a one-line delegation: `return loadConfigResolved(cwd, options).config`
- Exports `loadConfigResolved` in the `export =` block

Part 2 — init.cts cmdAgentSkills:
- Imports `findProjectRoot` from `./project-root.cjs`
- Anchors to project root before loading config (fixes #1366 cwd-drift)
- Uses `loadConfigResolved` for provenance; passes projectRoot to buildAgentSkillsBlock
- Computes `configured` + `reason` (AgentSkillsReason enum): 'resolved' |
  'not_configured' | 'configured_empty' | 'configured_unresolved'
- configured_empty and configured_unresolved emit stderr WARNING; not_configured is silent
- --json IR gains: configured, reason, source, degraded (in addition to existing
  agent_type, block, skills_count, warnings)

Tests (TDD):
- tests/config-loader.test.cjs: 8 new provenance tests (RED before impl, GREEN after)
- tests/agent-skills.test.cjs: 7 new diagnostic tests (RED before impl, GREEN after)
- All 306 tests across 4 suites pass (config-loader:33, agent-skills:72, init:105, workstream:96)

Docs:
- CONTEXT.md: Config Loader Module entry updated with loadConfigResolved interface;
  Resolution Provenance entry notes P2 is now implemented
- docs/CLI-TOOLS.md: --json field reference table added for agent-skills

Closes #1366
Part of #1411

Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>

src/init.cts

@@ -14,6 +14,7 @@ import { execGit, platformWriteSync, platformReadSync } from './shell-command-pr
 import io = require('./io.cjs');
 // eslint-disable-next-line @typescript-eslint/no-require-imports -- config-loader.cjs is an export= CommonJS module
 import configLoader = require('./config-loader.cjs');
+import { findProjectRoot } from './project-root.cjs';
 // eslint-disable-next-line @typescript-eslint/no-require-imports -- model-resolver.cjs is an export= CommonJS module
 import modelResolver = require('./model-resolver.cjs');
 // eslint-disable-next-line @typescript-eslint/no-require-imports -- phase-locator.cjs is an export= CommonJS module
@@ -47,7 +48,7 @@ import gitBaseBranch = require('./git-base-branch.cjs');
 const { gitWorktreeInfoInternal } = gitBaseBranch;
 
 const { output, error } = io;
-const { loadConfig } = configLoader;
+const { loadConfig, loadConfigResolved } = configLoader;
 const { resolveModelInternal, resolveGranularityInternal, assertValidGranularityOverride } = modelResolver;
 const { findPhaseInternal } = phaseLocator;
 const {
@@ -2015,6 +2016,9 @@ function buildAgentSkillsBlock(
   return `<agent_skills>\nRead these user-configured skills:\n${lines}\n</agent_skills>`;
 }
 
+/** Reason enum for agent-skills diagnostic (#1415, ADR-1411 P2). */
+type AgentSkillsReason = 'resolved' | 'not_configured' | 'configured_empty' | 'configured_unresolved';
+
 function cmdAgentSkills(
   cwd: string,
   agentType: string | undefined,
@@ -2026,24 +2030,67 @@ function cmdAgentSkills(
     return;
   }
 
-  const config = loadConfig(cwd);
+  // Anchor to project root before loading config (#1415/#1366 cwd-drift fix).
+  const projectRoot = findProjectRoot(cwd);
+  const { config, source, degraded } = loadConfigResolved(projectRoot);
   const diagnostics = { warnings: [] as string[] };
   const block = buildAgentSkillsBlock(
     config,
     agentType,
-    cwd,
+    projectRoot,
     diagnostics,
   );
 
+  // Compute configured + reason for diagnostic output.
+  const agentSkillsMap = (config && config['agent_skills'] && typeof config['agent_skills'] === 'object')
+    ? config['agent_skills'] as Record<string, unknown>
+    : {};
+  const configured = Object.prototype.hasOwnProperty.call(agentSkillsMap, agentType);
+
+  let reason: AgentSkillsReason;
+  let skillPaths: unknown = configured ? agentSkillsMap[agentType] : [];
+  if (!configured) {
+    reason = 'not_configured';
+    skillPaths = [];
+  } else {
+    // Normalize paths to array
+    if (typeof skillPaths === 'string') skillPaths = [skillPaths];
+    if (!Array.isArray(skillPaths)) skillPaths = [];
+    const pathsArr = skillPaths as unknown[];
+    // Fix 3: treat "" (empty string) as configured_empty — all-blank entries = no meaningful paths.
+    // An array of all empty/blank strings has length > 0 but zero meaningful paths.
+    const nonBlankPaths = pathsArr.filter(p => typeof p === 'string' && p.trim().length > 0);
+    if (pathsArr.length === 0 || nonBlankPaths.length === 0) {
+      // configured with empty array / "" / all-blank entries
+      reason = 'configured_empty';
+      // Reflect zero meaningful paths in the normalized array used for skills_count
+      skillPaths = [];
+      try {
+        process.stderr.write(
+          `[agent-skills] WARNING: Agent "${agentType}" is configured in agent_skills but has no skill paths — skills_count will be 0\n`
+        );
+      } catch { /* stderr might be closed */ }
+    } else if (!block) {
+      // configured with paths but all failed to resolve (warnings already emitted by buildAgentSkillsBlock)
+      reason = 'configured_unresolved';
+    } else {
+      reason = 'resolved';
+    }
+  }
+
+  const normalizedPaths = Array.isArray(skillPaths) ? skillPaths : [];
+
   if (jsonMode) {
-    const skillPaths =
-      (config && config.agent_skills && (config.agent_skills as Record<string, unknown>)[agentType]) || [];
-    const normalizedPaths = Array.isArray(skillPaths)
-      ? skillPaths
-      : skillPaths
-        ? [skillPaths]
-        : [];
-    output({ agent_type: agentType, block: block || '', skills_count: normalizedPaths.length, warnings: diagnostics.warnings }, raw);
+    output({
+      agent_type: agentType,
+      block: block || '',
+      skills_count: normalizedPaths.length,
+      warnings: diagnostics.warnings,
+      configured,
+      reason,
+      source,
+      degraded,
+    }, raw);
     return;
   }