@phren/cli 0.0.10 → 0.0.11

package/README.md

@@ -5,6 +5,8 @@
 <p align="center">
   <a href="https://www.npmjs.com/package/@phren/cli"><img src="https://img.shields.io/npm/v/%40phren%2Fcli?style=flat&labelColor=0D0D0D&color=7C3AED" alt="npm version"></a>
   <a href="https://github.com/alaarab/phren/blob/main/LICENSE"><img src="https://img.shields.io/github/license/alaarab/phren?style=flat&labelColor=0D0D0D&color=7C3AED" alt="license"></a>
+  <a href="https://alaarab.github.io/phren/"><img src="https://img.shields.io/badge/docs-alaarab.github.io%2Fphren-7C3AED?style=flat&labelColor=0D0D0D" alt="docs"></a>
+  <a href="https://alaarab.github.io/phren/whitepaper.pdf"><img src="https://img.shields.io/badge/whitepaper-PDF-7C3AED?style=flat&labelColor=0D0D0D" alt="whitepaper"></a>
 </p>
 
 <p align="center">
@@ -47,14 +49,6 @@ Init detects your tools, registers MCP servers, and installs lifecycle hooks. Af
 
 To add a project later, run `phren add` from that directory. To browse what phren knows, run `phren` to open the interactive shell.
 
-## Learn more
-
-- [Documentation site](https://alaarab.github.io/phren/)
-- [Whitepaper (PDF)](https://alaarab.github.io/phren/whitepaper.pdf)
-- [Architecture](docs/architecture.md) — how retrieval, governance, and persistence fit together
-- [Contributing](CONTRIBUTING.md) — how to add tools, skills, and tests
-- [Security](SECURITY.md)
-
 ---
 
 MIT License. Made by [Ala Arab](https://github.com/alaarab).

package/mcp/dist/cli-actions.js

@@ -58,7 +58,7 @@ export async function handleAddFinding(project, learning) {
         console.log(result.message);
     }
     catch (err) {
-        console.error(err instanceof Error ? err.message : String(err));
+        console.error(errorMessage(err));
         process.exit(1);
     }
 }
@@ -164,7 +164,7 @@ export async function handleDoctor(args) {
                         }
                     }
                     catch (err) {
-                        if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
+                        if ((process.env.PHREN_DEBUG))
                             process.stderr.write(`[phren] doctor searchMissParse: ${errorMessage(err)}\n`);
                     }
                 }
@@ -181,7 +181,7 @@ export async function handleDoctor(args) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
+        if ((process.env.PHREN_DEBUG))
             process.stderr.write(`[phren] doctor searchMissAnalysis: ${errorMessage(err)}\n`);
     }
     try {
@@ -215,7 +215,7 @@ export async function handleDoctor(args) {
         }
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
+        if ((process.env.PHREN_DEBUG))
             process.stderr.write(`[phren] doctor ollamaStatus: ${errorMessage(err)}\n`);
     }
     process.exit(result.ok ? 0 : 1);
@@ -257,7 +257,7 @@ export async function handleStatus() {
         console.log(`semantic-search: ${model} ready, ${formatEmbeddingCoverage(coverage)}`);
     }
     catch (err) {
-        if ((process.env.PHREN_DEBUG || process.env.PHREN_DEBUG))
+        if ((process.env.PHREN_DEBUG))
             process.stderr.write(`[phren] handleStatus semanticSearch: ${errorMessage(err)}\n`);
     }
 }

package/mcp/dist/cli-config.js

@@ -1,17 +1,132 @@
 import { getPhrenPath, readRootManifest } from "./shared.js";
 import { installPreferencesFile } from "./phren-paths.js";
-import { getIndexPolicy, updateIndexPolicy, getRetentionPolicy, updateRetentionPolicy, getWorkflowPolicy, updateWorkflowPolicy, } from "./shared-governance.js";
-import { listMachines as listMachinesStore, listProfiles as listProfilesStore } from "./data-access.js";
+import { getIndexPolicy, updateIndexPolicy, getRetentionPolicy, updateRetentionPolicy, getWorkflowPolicy, updateWorkflowPolicy, mergeConfig, VALID_TASK_MODES, VALID_FINDING_SENSITIVITY, } from "./shared-governance.js";
+import { listMachines as listMachinesStore, listProfiles as listProfilesStore, listProfiles } from "./data-access.js";
 import { setTelemetryEnabled, getTelemetrySummary, resetTelemetry } from "./telemetry.js";
 import { governanceInstallPreferencesFile, readInstallPreferences, readGovernanceInstallPreferences, writeInstallPreferences, writeGovernanceInstallPreferences, } from "./init-preferences.js";
 import { PROACTIVITY_LEVELS, getProactivityLevel, getProactivityLevelForTask, getProactivityLevelForFindings, } from "./proactivity.js";
-import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, parseProjectOwnershipMode, } from "./project-config.js";
+import { PROJECT_OWNERSHIP_MODES, getProjectOwnershipDefault, parseProjectOwnershipMode, updateProjectConfigOverrides, } from "./project-config.js";
 import { isValidProjectName, learnedSynonymsPath, learnSynonym, loadLearnedSynonyms, removeLearnedSynonym, } from "./utils.js";
+// ── Shared helpers ────────────────────────────────────────────────────────────
+export function parseProjectArg(args) {
+    const project = args.find((a) => a.startsWith("--project="))?.slice("--project=".length)
+        ?? (args.indexOf("--project") !== -1 ? args[args.indexOf("--project") + 1] : undefined);
+    const rest = args.filter((a, i) => a !== "--project" && !a.startsWith("--project=") && args[i - 1] !== "--project");
+    return { project, rest };
+}
+export function checkProjectInProfile(phrenPath, project) {
+    const profiles = listProfiles(phrenPath);
+    if (profiles.ok) {
+        const registered = profiles.data.some((entry) => entry.projects.includes(project));
+        if (!registered) {
+            return `Warning: Project '${project}' not found in active profile. Run 'phren add /path/to/${project}' first.\n  Config was written to ${phrenPath}/${project}/phren.project.yaml but won't be used until the project is registered.`;
+        }
+    }
+    return null;
+}
+function warnIfUnregistered(phrenPath, project) {
+    const warning = checkProjectInProfile(phrenPath, project);
+    if (warning)
+        console.error(warning);
+}
+export function buildProactivitySnapshot(phrenPath) {
+    const prefs = readGovernanceInstallPreferences(phrenPath);
+    return {
+        path: governanceInstallPreferencesFile(phrenPath),
+        configured: {
+            proactivity: prefs.proactivity ?? null,
+            proactivityFindings: prefs.proactivityFindings ?? null,
+            proactivityTask: prefs.proactivityTask ?? null,
+        },
+        effective: {
+            proactivity: getProactivityLevel(phrenPath),
+            proactivityFindings: getProactivityLevelForFindings(phrenPath),
+            proactivityTask: getProactivityLevelForTask(phrenPath),
+        },
+    };
+}
+// ── Config show ───────────────────────────────────────────────────────────────
+function formatConfigAsTable(label, rows) {
+    const maxKey = Math.max(...rows.map(([k]) => k.length));
+    console.log(`\n${label}`);
+    for (const [k, v] of rows) {
+        console.log(`  ${k.padEnd(maxKey)}  ${v}`);
+    }
+}
+export function handleConfigShow(args) {
+    const phrenPath = getPhrenPath();
+    const { project: projectArg } = parseProjectArg(args);
+    if (projectArg) {
+        if (!isValidProjectName(projectArg)) {
+            console.error(`Invalid project name: "${projectArg}"`);
+            process.exit(1);
+        }
+        const resolved = mergeConfig(phrenPath, projectArg);
+        const inProfile = checkProjectInProfile(phrenPath, projectArg);
+        console.log(`\nConfig for project: ${projectArg}${inProfile ? "" : "  (not in active profile)"}`);
+        formatConfigAsTable("Finding capture", [
+            ["sensitivity", resolved.findingSensitivity],
+            ["proactivity", resolved.proactivity.base ?? "(global)"],
+            ["proactivity.findings", resolved.proactivity.findings ?? "(global)"],
+            ["proactivity.tasks", resolved.proactivity.tasks ?? "(global)"],
+        ]);
+        formatConfigAsTable("Task automation", [
+            ["taskMode", resolved.taskMode],
+        ]);
+        formatConfigAsTable("Retention policy", [
+            ["ttlDays", String(resolved.retentionPolicy.ttlDays)],
+            ["retentionDays", String(resolved.retentionPolicy.retentionDays)],
+            ["autoAcceptThreshold", String(resolved.retentionPolicy.autoAcceptThreshold)],
+            ["minInjectConfidence", String(resolved.retentionPolicy.minInjectConfidence)],
+            ["decay.d30", String(resolved.retentionPolicy.decay.d30)],
+            ["decay.d60", String(resolved.retentionPolicy.decay.d60)],
+            ["decay.d90", String(resolved.retentionPolicy.decay.d90)],
+            ["decay.d120", String(resolved.retentionPolicy.decay.d120)],
+        ]);
+        formatConfigAsTable("Workflow policy", [
+            ["lowConfidenceThreshold", String(resolved.workflowPolicy.lowConfidenceThreshold)],
+            ["riskySections", resolved.workflowPolicy.riskySections.join(", ")],
+        ]);
+        if (!inProfile) {
+            console.error(`\nRun 'phren add /path/to/${projectArg}' to register this project.`);
+        }
+        console.log("");
+        return;
+    }
+    // Global config — no project
+    const retention = getRetentionPolicy(phrenPath);
+    const workflow = getWorkflowPolicy(phrenPath);
+    console.log("\nGlobal config (applies to all projects unless overridden)");
+    formatConfigAsTable("Finding capture", [
+        ["findingSensitivity", workflow.findingSensitivity],
+    ]);
+    formatConfigAsTable("Task automation", [
+        ["taskMode", workflow.taskMode],
+    ]);
+    formatConfigAsTable("Retention policy", [
+        ["ttlDays", String(retention.ttlDays)],
+        ["retentionDays", String(retention.retentionDays)],
+        ["autoAcceptThreshold", String(retention.autoAcceptThreshold)],
+        ["minInjectConfidence", String(retention.minInjectConfidence)],
+        ["decay.d30", String(retention.decay.d30)],
+        ["decay.d60", String(retention.decay.d60)],
+        ["decay.d90", String(retention.decay.d90)],
+        ["decay.d120", String(retention.decay.d120)],
+    ]);
+    formatConfigAsTable("Workflow policy", [
+        ["lowConfidenceThreshold", String(workflow.lowConfidenceThreshold)],
+        ["riskySections", workflow.riskySections.join(", ")],
+    ]);
+    console.log(`\nUse '--project <name>' to see merged config for a specific project.`);
+    console.log("");
+}
 // ── Config router ────────────────────────────────────────────────────────────
 export async function handleConfig(args) {
     const sub = args[0];
     const rest = args.slice(1);
     switch (sub) {
+        case "show":
+            return handleConfigShow(rest);
         case "policy":
             return handleRetentionPolicy(rest);
         case "workflow":
@@ -42,6 +157,7 @@ export async function handleConfig(args) {
             console.log(`phren config - manage settings and policies
 
 Subcommands:
+  phren config show [--project <name>]  Full merged config summary (what's actually active)
   phren config policy [get|set ...]     Memory retention, TTL, confidence, decay
   phren config workflow [get|set ...]   Risky-memory thresholds, task automation mode
   phren config index [get|set ...]      Indexer include/exclude globs
@@ -137,30 +253,30 @@ function handleConfigSynonyms(args) {
     printSynonymsUsage();
     process.exit(1);
 }
-function proactivityConfigSnapshot(phrenPath) {
-    const prefs = readGovernanceInstallPreferences(phrenPath);
-    return {
-        path: governanceInstallPreferencesFile(phrenPath),
-        configured: {
-            proactivity: prefs.proactivity ?? null,
-            proactivityFindings: prefs.proactivityFindings ?? null,
-            proactivityTask: prefs.proactivityTask ?? null,
-        },
-        effective: {
-            proactivity: getProactivityLevel(phrenPath),
-            proactivityFindings: getProactivityLevelForFindings(phrenPath),
-            proactivityTask: getProactivityLevelForTask(phrenPath),
-        },
-    };
-}
+const proactivityConfigSnapshot = buildProactivitySnapshot;
 function handleConfigProactivity(subcommand, args) {
     const phrenPath = getPhrenPath();
-    const value = args[0];
+    const { project: projectArg, rest: filteredArgs } = parseProjectArg(args);
+    const value = filteredArgs[0];
     if (value === undefined) {
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
+                process.exit(1);
+            }
+            const resolved = mergeConfig(phrenPath, projectArg);
+            console.log(JSON.stringify({
+                _project: projectArg,
+                base: resolved.proactivity.base ?? null,
+                findings: resolved.proactivity.findings ?? null,
+                tasks: resolved.proactivity.tasks ?? null,
+            }, null, 2));
+            return;
+        }
         console.log(JSON.stringify(proactivityConfigSnapshot(phrenPath), null, 2));
         return;
     }
-    if (args.length !== 1) {
+    if (filteredArgs.length !== 1) {
         printProactivityUsage(subcommand);
         process.exit(1);
     }
@@ -169,6 +285,25 @@ function handleConfigProactivity(subcommand, args) {
         printProactivityUsage(subcommand);
         process.exit(1);
     }
+    if (projectArg) {
+        if (!isValidProjectName(projectArg)) {
+            console.error(`Invalid project name: "${projectArg}"`);
+            process.exit(1);
+        }
+        warnIfUnregistered(phrenPath, projectArg);
+        const key = subcommand === "proactivity" ? "proactivity"
+            : subcommand === "proactivity.findings" ? "proactivityFindings"
+                : "proactivityTask";
+        updateProjectConfigOverrides(phrenPath, projectArg, (current) => ({ ...current, [key]: level }));
+        const resolved = mergeConfig(phrenPath, projectArg);
+        console.log(JSON.stringify({
+            _project: projectArg,
+            base: resolved.proactivity.base ?? null,
+            findings: resolved.proactivity.findings ?? null,
+            tasks: resolved.proactivity.tasks ?? null,
+        }, null, 2));
+        return;
+    }
     switch (subcommand) {
         case "proactivity":
             writeGovernanceInstallPreferences(phrenPath, { proactivity: level });
@@ -213,61 +348,7 @@ function handleConfigProjectOwnership(args) {
     writeInstallPreferences(phrenPath, { projectOwnershipDefault: ownership });
     console.log(JSON.stringify(projectOwnershipConfigSnapshot(phrenPath), null, 2));
 }
-// ── Task mode ─────────────────────────────────────────────────────────────────
-const TASK_MODES = ["off", "manual", "suggest", "auto"];
-function normalizeTaskMode(raw) {
-    if (!raw)
-        return undefined;
-    const normalized = raw.trim().toLowerCase();
-    return TASK_MODES.includes(normalized) ? normalized : undefined;
-}
-function taskModeConfigSnapshot(phrenPath) {
-    const policy = getWorkflowPolicy(phrenPath);
-    return {
-        taskMode: policy.taskMode,
-    };
-}
-function handleConfigTaskMode(args) {
-    const phrenPath = getPhrenPath();
-    const action = args[0];
-    if (!action || action === "get") {
-        console.log(JSON.stringify(taskModeConfigSnapshot(phrenPath), null, 2));
-        return;
-    }
-    if (action === "set") {
-        const mode = normalizeTaskMode(args[1]);
-        if (!mode) {
-            console.error(`Usage: phren config task-mode set [${TASK_MODES.join("|")}]`);
-            process.exit(1);
-        }
-        const result = updateWorkflowPolicy(phrenPath, { taskMode: mode });
-        if (!result.ok) {
-            console.error(result.error);
-            if (result.code === "PERMISSION_DENIED")
-                process.exit(1);
-            return;
-        }
-        console.log(JSON.stringify(taskModeConfigSnapshot(phrenPath), null, 2));
-        return;
-    }
-    // Bare value: phren config task-mode auto
-    const mode = normalizeTaskMode(action);
-    if (mode) {
-        const result = updateWorkflowPolicy(phrenPath, { taskMode: mode });
-        if (!result.ok) {
-            console.error(result.error);
-            if (result.code === "PERMISSION_DENIED")
-                process.exit(1);
-            return;
-        }
-        console.log(JSON.stringify(taskModeConfigSnapshot(phrenPath), null, 2));
-        return;
-    }
-    console.error(`Usage: phren config task-mode [get|set <mode>|<mode>]  — modes: ${TASK_MODES.join("|")}`);
-    process.exit(1);
-}
-// ── Finding sensitivity ───────────────────────────────────────────────────────
-const FINDING_SENSITIVITY_LEVELS = ["minimal", "conservative", "balanced", "aggressive"];
+// ── Finding sensitivity config ────────────────────────────────────────────────
 export const FINDING_SENSITIVITY_CONFIG = {
     minimal: {
         sessionCap: 0,
@@ -290,59 +371,94 @@ export const FINDING_SENSITIVITY_CONFIG = {
         agentInstruction: "Save everything worth remembering — err on the side of capturing.",
     },
 };
-function normalizeFindingSensitivity(v) {
-    if (!v)
-        return null;
-    const lower = v.toLowerCase();
-    if (FINDING_SENSITIVITY_LEVELS.includes(lower))
-        return lower;
-    return null;
-}
-function findingSensitivityConfigSnapshot(phrenPath) {
-    const policy = getWorkflowPolicy(phrenPath);
-    const level = policy.findingSensitivity;
-    const config = FINDING_SENSITIVITY_CONFIG[level];
-    return { level, ...config };
-}
-function handleConfigFindingSensitivity(args) {
+function handleWorkflowField(args, opts) {
     const phrenPath = getPhrenPath();
-    const action = args[0];
+    const { project: projectArg, rest: filteredArgs } = parseProjectArg(args);
+    const action = filteredArgs[0];
     if (!action || action === "get") {
-        console.log(JSON.stringify(findingSensitivityConfigSnapshot(phrenPath), null, 2));
-        return;
-    }
-    if (action === "set") {
-        const level = normalizeFindingSensitivity(args[1]);
-        if (!level) {
-            console.error(`Usage: phren config finding-sensitivity set [${FINDING_SENSITIVITY_LEVELS.join("|")}]`);
-            process.exit(1);
-        }
-        const result = updateWorkflowPolicy(phrenPath, { findingSensitivity: level });
-        if (!result.ok) {
-            console.error(result.error);
-            if (result.code === "PERMISSION_DENIED")
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
                 process.exit(1);
+            }
+            const resolved = mergeConfig(phrenPath, projectArg);
+            const value = opts.getProjectValue(resolved);
+            console.log(JSON.stringify(opts.formatProjectOutput(projectArg, value), null, 2));
             return;
         }
-        console.log(JSON.stringify(findingSensitivityConfigSnapshot(phrenPath), null, 2));
+        console.log(JSON.stringify(opts.getSnapshot(phrenPath), null, 2));
         return;
     }
-    // Bare value: phren config finding-sensitivity balanced
-    const level = normalizeFindingSensitivity(action);
-    if (level) {
-        const result = updateWorkflowPolicy(phrenPath, { findingSensitivity: level });
+    const applyValue = (value) => {
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
+                process.exit(1);
+            }
+            warnIfUnregistered(phrenPath, projectArg);
+            updateProjectConfigOverrides(phrenPath, projectArg, (current) => ({ ...current, [opts.projectOverrideKey]: value }));
+            const resolved = mergeConfig(phrenPath, projectArg);
+            const eff = opts.getProjectValue(resolved);
+            console.log(JSON.stringify(opts.formatProjectOutput(projectArg, eff), null, 2));
+            return;
+        }
+        const result = updateWorkflowPolicy(phrenPath, { [opts.workflowPatchKey]: value });
         if (!result.ok) {
             console.error(result.error);
             if (result.code === "PERMISSION_DENIED")
                 process.exit(1);
             return;
         }
-        console.log(JSON.stringify(findingSensitivityConfigSnapshot(phrenPath), null, 2));
-        return;
+        console.log(JSON.stringify(opts.getSnapshot(phrenPath), null, 2));
+    };
+    if (action === "set") {
+        const value = opts.normalize(filteredArgs[1]);
+        if (!value) {
+            console.error(`Usage: phren config ${opts.fieldName} set [${opts.validValues.join("|")}]`);
+            process.exit(1);
+        }
+        return applyValue(value);
     }
-    console.error(`Usage: phren config finding-sensitivity [get|set <level>|<level>]  — levels: ${FINDING_SENSITIVITY_LEVELS.join("|")}`);
+    const value = opts.normalize(action);
+    if (value)
+        return applyValue(value);
+    console.error(`Usage: phren config ${opts.fieldName} [--project <name>] [get|set <value>|<value>]  — values: ${opts.validValues.join("|")}`);
     process.exit(1);
 }
+function normalizeFromList(raw, validValues) {
+    if (!raw)
+        return null;
+    const lower = raw.trim().toLowerCase();
+    return validValues.includes(lower) ? lower : null;
+}
+function handleConfigTaskMode(args) {
+    handleWorkflowField(args, {
+        fieldName: "task-mode",
+        validValues: VALID_TASK_MODES,
+        normalize: (raw) => normalizeFromList(raw, VALID_TASK_MODES),
+        getSnapshot: (phrenPath) => ({ taskMode: getWorkflowPolicy(phrenPath).taskMode }),
+        getProjectValue: (resolved) => resolved.taskMode,
+        formatProjectOutput: (proj, value) => ({ _project: proj, taskMode: value }),
+        workflowPatchKey: "taskMode",
+        projectOverrideKey: "taskMode",
+    });
+}
+function handleConfigFindingSensitivity(args) {
+    handleWorkflowField(args, {
+        fieldName: "finding-sensitivity",
+        validValues: VALID_FINDING_SENSITIVITY,
+        normalize: (raw) => normalizeFromList(raw, VALID_FINDING_SENSITIVITY),
+        getSnapshot: (phrenPath) => {
+            const policy = getWorkflowPolicy(phrenPath);
+            const level = policy.findingSensitivity;
+            return { level, ...FINDING_SENSITIVITY_CONFIG[level] };
+        },
+        getProjectValue: (resolved) => resolved.findingSensitivity,
+        formatProjectOutput: (proj, value) => ({ _project: proj, level: value, ...FINDING_SENSITIVITY_CONFIG[value] }),
+        workflowPatchKey: "findingSensitivity",
+        projectOverrideKey: "findingSensitivity",
+    });
+}
 // ── LLM config ───────────────────────────────────────────────────────────────
 const EXPENSIVE_MODEL_RE = /opus|sonnet|gpt-4(?!o-mini)/i;
 const DEFAULT_LLM_MODEL = "gpt-4o-mini / claude-haiku-4-5-20251001";
@@ -442,10 +558,20 @@ export async function handleIndexPolicy(args) {
 }
 // ── Memory policy ────────────────────────────────────────────────────────────
 export async function handleRetentionPolicy(args) {
-    if (!args.length || args[0] === "get") {
-        console.log(JSON.stringify(getRetentionPolicy(getPhrenPath()), null, 2));
-        const dedupOn = (process.env.PHREN_FEATURE_SEMANTIC_DEDUP ?? (process.env.PHREN_FEATURE_SEMANTIC_DEDUP || process.env.PHREN_FEATURE_SEMANTIC_DEDUP)) === "1";
-        const conflictOn = (process.env.PHREN_FEATURE_SEMANTIC_CONFLICT ?? (process.env.PHREN_FEATURE_SEMANTIC_CONFLICT || process.env.PHREN_FEATURE_SEMANTIC_CONFLICT)) === "1";
+    const phrenPath = getPhrenPath();
+    const { project: projectArg, rest: filteredArgs } = parseProjectArg(args);
+    if (!filteredArgs.length || filteredArgs[0] === "get") {
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
+                process.exit(1);
+            }
+            const resolved = mergeConfig(phrenPath, projectArg);
+            console.log(JSON.stringify({ _project: projectArg, ...resolved.retentionPolicy }, null, 2));
+            return;
+        }
+        console.log(JSON.stringify(getRetentionPolicy(phrenPath), null, 2));
+        const conflictOn = process.env.PHREN_FEATURE_SEMANTIC_CONFLICT === "1";
         process.stderr.write(`\nDedup: free Jaccard similarity scan on every add_finding (no API key needed).\n`);
         process.stderr.write(`  Near-matches (30–55% overlap) are returned in the response for the agent to decide.\n`);
         if (conflictOn) {
@@ -458,9 +584,40 @@ export async function handleRetentionPolicy(args) {
         }
         return;
     }
-    if (args[0] === "set") {
+    if (filteredArgs[0] === "set") {
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
+                process.exit(1);
+            }
+            warnIfUnregistered(phrenPath, projectArg);
+            updateProjectConfigOverrides(phrenPath, projectArg, (current) => {
+                const existingRetention = current.retentionPolicy ?? {};
+                const retentionPatch = { ...existingRetention };
+                for (const arg of filteredArgs.slice(1)) {
+                    if (!arg.startsWith("--"))
+                        continue;
+                    const [k, v] = arg.slice(2).split("=");
+                    if (!k || v === undefined)
+                        continue;
+                    const num = Number(v);
+                    const value = Number.isNaN(num) ? v : num;
+                    if (k.startsWith("decay.")) {
+                        retentionPatch.decay = { ...(retentionPatch.decay ?? {}) };
+                        retentionPatch.decay[k.slice("decay.".length)] = value;
+                    }
+                    else {
+                        retentionPatch[k] = value;
+                    }
+                }
+                return { ...current, retentionPolicy: retentionPatch };
+            });
+            const resolved = mergeConfig(phrenPath, projectArg);
+            console.log(JSON.stringify({ _project: projectArg, ...resolved.retentionPolicy }, null, 2));
+            return;
+        }
         const patch = {};
-        for (const arg of args.slice(1)) {
+        for (const arg of filteredArgs.slice(1)) {
             if (!arg.startsWith("--"))
                 continue;
             const [k, v] = arg.slice(2).split("=");
@@ -476,7 +633,7 @@ export async function handleRetentionPolicy(args) {
                 patch[k] = value;
             }
         }
-        const result = updateRetentionPolicy(getPhrenPath(), patch);
+        const result = updateRetentionPolicy(phrenPath, patch);
         if (!result.ok) {
             console.log(result.error);
             if (result.code === "PERMISSION_DENIED")
@@ -486,18 +643,68 @@ export async function handleRetentionPolicy(args) {
         console.log(JSON.stringify(result.data, null, 2));
         return;
     }
-    console.error("Usage: phren config policy [get|set --ttlDays=120 --retentionDays=365 --autoAcceptThreshold=0.75 --minInjectConfidence=0.35 --decay.d30=1 --decay.d60=0.85 --decay.d90=0.65 --decay.d120=0.45]");
+    console.error("Usage: phren config policy [--project <name>] [get|set --ttlDays=120 --retentionDays=365 --autoAcceptThreshold=0.75 --minInjectConfidence=0.35 --decay.d30=1 --decay.d60=0.85 --decay.d90=0.65 --decay.d120=0.45]");
     process.exit(1);
 }
 // ── Memory workflow ──────────────────────────────────────────────────────────
 export async function handleWorkflowPolicy(args) {
-    if (!args.length || args[0] === "get") {
-        console.log(JSON.stringify(getWorkflowPolicy(getPhrenPath()), null, 2));
+    const phrenPath = getPhrenPath();
+    const { project: projectArg, rest: filteredArgs } = parseProjectArg(args);
+    if (!filteredArgs.length || filteredArgs[0] === "get") {
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
+                process.exit(1);
+            }
+            const resolved = mergeConfig(phrenPath, projectArg);
+            console.log(JSON.stringify({ _project: projectArg, ...resolved.workflowPolicy }, null, 2));
+            return;
+        }
+        console.log(JSON.stringify(getWorkflowPolicy(phrenPath), null, 2));
         return;
     }
-    if (args[0] === "set") {
+    if (filteredArgs[0] === "set") {
+        if (projectArg) {
+            if (!isValidProjectName(projectArg)) {
+                console.error(`Invalid project name: "${projectArg}"`);
+                process.exit(1);
+            }
+            warnIfUnregistered(phrenPath, projectArg);
+            updateProjectConfigOverrides(phrenPath, projectArg, (current) => {
+                const nextConfig = { ...current };
+                const existingWorkflow = current.workflowPolicy ?? {};
+                const workflowPatch = { ...existingWorkflow };
+                for (const arg of filteredArgs.slice(1)) {
+                    if (!arg.startsWith("--"))
+                        continue;
+                    const [k, v] = arg.slice(2).split("=");
+                    if (!k || v === undefined)
+                        continue;
+                    if (k === "riskySections") {
+                        workflowPatch.riskySections = v.split(",").map((s) => s.trim()).filter(Boolean);
+                    }
+                    else if (k === "taskMode") {
+                        nextConfig.taskMode = v;
+                    }
+                    else if (k === "findingSensitivity") {
+                        nextConfig.findingSensitivity = v;
+                    }
+                    else {
+                        const num = Number(v);
+                        workflowPatch[k] = Number.isNaN(num) ? v : num;
+                    }
+                }
+                if (Object.keys(workflowPatch).length > 0 || existingWorkflow !== current.workflowPolicy) {
+                    nextConfig.workflowPolicy = workflowPatch;
+                }
+                return nextConfig;
+            });
+            const resolved = mergeConfig(phrenPath, projectArg);
+            console.log(JSON.stringify({ _project: projectArg, ...resolved.workflowPolicy }, null, 2));
+            return;
+        }
         const patch = {};
-        for (const arg of args.slice(1)) {
+        for (const arg of filteredArgs.slice(1)) {
             if (!arg.startsWith("--"))
                 continue;
             const [k, v] = arg.slice(2).split("=");
@@ -511,7 +718,7 @@ export async function handleWorkflowPolicy(args) {
                 patch[k] = Number.isNaN(num) ? v : num;
             }
         }
-        const result = updateWorkflowPolicy(getPhrenPath(), patch);
+        const result = updateWorkflowPolicy(phrenPath, patch);
         if (!result.ok) {
             console.log(result.error);
             if (result.code === "PERMISSION_DENIED")
@@ -521,7 +728,7 @@ export async function handleWorkflowPolicy(args) {
         console.log(JSON.stringify(result.data, null, 2));
         return;
     }
-    console.error("Usage: phren config workflow [get|set --lowConfidenceThreshold=0.7 --riskySections=Stale,Conflicts --taskMode=manual]");
+    console.error("Usage: phren config workflow [--project <name>] [get|set --lowConfidenceThreshold=0.7 --riskySections=Stale,Conflicts --taskMode=manual]");
     process.exit(1);
 }
 // ── Machines and profiles ────────────────────────────────────────────────────