@danielmarbach/mnemonic-mcp 0.9.0 → 0.10.0

package/CHANGELOG.md

@@ -4,6 +4,17 @@ All notable changes to `mnemonic` will be documented in this file.
 
 The format is loosely based on Keep a Changelog and uses semver-style version headings.
 
+## [0.10.0] - 2026-03-14
+
+### Changed
+
+- Performance in hot read paths: `recall` now reuses note reads within a single request instead of re-reading the same note during scoring and formatting.
+- Consolidation analysis (`detect-duplicates`, `suggest-merges`) now preloads embeddings once per note and reuses vectors during pairwise similarity checks.
+- `Storage.listNotes` and `Storage.listEmbeddings` now load files in parallel to reduce serialized disk I/O while preserving existing output behavior.
+- `VaultManager.searchOrder` now avoids duplicate git-root resolution in a single call, reducing unnecessary git subprocess work in read-heavy flows.
+- Mutating tools now return deterministic retry metadata when a git commit fails after the mutation is already written, including attempted commit message/body/files and retry safety hints.
+- Commit persistence reporting now includes explicit commit-failure details (`git.commit=failed` with `commitError`) so recovery can be automated without reconstructing commit intent.
+
 ## [0.9.0] - 2026-03-14
 
 ### Added

package/build/git.d.ts

@@ -11,12 +11,13 @@ export interface SyncResult {
     pushedCommits: number;
 }
 export interface CommitResult {
-    status: "committed" | "skipped";
-    reason?: "git-disabled" | "no-changes";
+    status: "committed" | "skipped" | "failed";
+    reason?: "git-disabled" | "no-changes" | "error";
+    error?: string;
 }
 export interface PushResult {
     status: "pushed" | "skipped" | "failed";
-    reason?: "git-disabled" | "no-remote" | "auto-push-disabled";
+    reason?: "git-disabled" | "no-remote" | "auto-push-disabled" | "commit-failed";
     error?: string;
 }
 export declare class GitOps {

package/build/git.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"git.d.ts","sourceRoot":"","sources":["../src/git.ts"],"names":[],"mappings":"AAEA,qBAAa,iBAAkB,SAAQ,KAAK;gBAC9B,SAAS,EAAE,QAAQ,GAAG,MAAM,EAAE,KAAK,EAAE,OAAO;CAKzD;AAED,MAAM,WAAW,UAAU;IACzB,SAAS,EAAE,OAAO,CAAC;IACnB,uEAAuE;IACvE,aAAa,EAAE,MAAM,EAAE,CAAC;IACxB,2CAA2C;IAC3C,cAAc,EAAE,MAAM,EAAE,CAAC;IACzB,+CAA+C;IAC/C,aAAa,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,WAAW,GAAG,SAAS,GAAG,QAAQ,CAAC;IAC3C,MAAM,CAAC,EAAE,cAAc,GAAG,YAAY,GAAG,OAAO,CAAC;IACjD,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,UAAU;IACzB,MAAM,EAAE,QAAQ,GAAG,SAAS,GAAG,QAAQ,CAAC;IACxC,MAAM,CAAC,EAAE,cAAc,GAAG,WAAW,GAAG,oBAAoB,GAAG,eAAe,CAAC;IAC/E,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,qBAAa,MAAM;IACjB,OAAO,CAAC,GAAG,CAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC;;;OAGG;IACH,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAS;IACrC,OAAO,CAAC,OAAO,CAAU;gBAEb,OAAO,EAAE,MAAM,EAAE,WAAW,GAAE,MAAgB;IAMpD,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAY3B;;;;;;;;;;;;;;;;;;OAkBG;IACG,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC;IAQzE,gBAAgB,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC;IAyB9F;;;;OAIG;IACG,IAAI,IAAI,OAAO,CAAC,UAAU,CAAC;IA6BjC,uEAAuE;IACjE,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAIrB,cAAc,IAAI,OAAO,CAAC,UAAU,CAAC;YAiB7B,WAAW;YASX,oBAAoB;IASlC;;;OAGG;YACW,cAAc;CAuC7B"}

package/build/git.js

@@ -53,6 +53,9 @@ export class GitOps {
      */
     async commit(message, files, body) {
         const result = await this.commitWithStatus(message, files, body);
+        if (result.status === "failed") {
+            throw new GitOperationError("commit", result.error ?? "unknown commit failure");
+        }
         return result.status === "committed";
     }
     async commitWithStatus(message, files, body) {
@@ -75,8 +78,9 @@ export class GitOps {
             return { status: "committed" };
         }
         catch (err) {
-            console.error(`[git] Commit failed: ${err}`);
-            throw new GitOperationError("commit", err);
+            const message = err instanceof Error ? err.message : String(err);
+            console.error(`[git] Commit failed: ${message}`);
+            return { status: "failed", reason: "error", error: message };
         }
     }
     /**

package/build/git.js.map

@@ -1 +1 @@
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package/build/index.js

@@ -592,12 +592,34 @@ function buildPersistenceStatus(args) {
             commitMessage: args.commitMessage,
             commitBody: args.commitBody,
             commitReason: args.commit.reason,
+            commitError: args.commit.error,
             pushReason: args.push.reason,
             pushError: args.push.error,
         },
+        retry: args.retry,
         durability: resolveDurability(args.commit, args.push),
     };
 }
+function buildMutationRetryContract(args) {
+    if (args.commit.status !== "failed") {
+        return undefined;
+    }
+    return {
+        attemptedCommit: {
+            message: args.commitMessage,
+            body: args.commitBody,
+            files: args.files,
+            cwd: args.cwd,
+            vault: storageLabel(args.vault),
+            error: args.commit.error ?? "Unknown git commit failure",
+        },
+        mutationApplied: args.mutationApplied,
+        retrySafe: args.mutationApplied,
+        rationale: args.mutationApplied
+            ? "Mutation is already persisted on disk; commit can be retried deterministically."
+            : "Mutation was not applied; retry may require re-running the operation.",
+    };
+}
 function formatPersistenceSummary(persistence) {
     const parts = [
         `Persistence: embedding ${persistence.embedding.status}`,
@@ -716,7 +738,7 @@ async function formatProjectPolicyLine(projectId) {
     }
     return `Policy: default write scope ${policy.defaultScope} (updated ${policy.updatedAt})`;
 }
-async function moveNoteBetweenVaults(found, targetVault, noteToWrite) {
+async function moveNoteBetweenVaults(found, targetVault, noteToWrite, cwd) {
     const { note, vault: sourceVault } = found;
     const finalNote = noteToWrite ?? note;
     const embedding = await sourceVault.storage.readEmbedding(note.id);
@@ -733,7 +755,9 @@ async function moveNoteBetweenVaults(found, targetVault, noteToWrite) {
         noteTitle: finalNote.title,
         projectName: finalNote.projectName,
     });
-    const targetCommit = await targetVault.git.commitWithStatus(`move: ${finalNote.title}`, [vaultManager.noteRelPath(targetVault, finalNote.id)], targetCommitBody);
+    const targetCommitMessage = `move: ${finalNote.title}`;
+    const targetCommitFiles = [vaultManager.noteRelPath(targetVault, finalNote.id)];
+    const targetCommit = await targetVault.git.commitWithStatus(targetCommitMessage, targetCommitFiles, targetCommitBody);
     const sourceCommitBody = formatCommitBody({
         summary: `Moved to ${targetVaultLabel}`,
         noteId: finalNote.id,
@@ -741,7 +765,18 @@ async function moveNoteBetweenVaults(found, targetVault, noteToWrite) {
         projectName: finalNote.projectName,
     });
     await sourceVault.git.commitWithStatus(`move: ${finalNote.title}`, [vaultManager.noteRelPath(sourceVault, finalNote.id)], sourceCommitBody);
-    const targetPush = await pushAfterMutation(targetVault);
+    const targetPush = targetCommit.status === "committed"
+        ? await pushAfterMutation(targetVault)
+        : { status: "skipped", reason: "commit-failed" };
+    const retry = buildMutationRetryContract({
+        commit: targetCommit,
+        commitMessage: targetCommitMessage,
+        commitBody: targetCommitBody,
+        files: targetCommitFiles,
+        cwd,
+        vault: targetVault,
+        mutationApplied: true,
+    });
     if (sourceVault !== targetVault) {
         await pushAfterMutation(sourceVault);
     }
@@ -753,8 +788,9 @@ async function moveNoteBetweenVaults(found, targetVault, noteToWrite) {
             embedding: embedding ? { status: "written" } : { status: "skipped", reason: "no-source-embedding" },
             commit: targetCommit,
             push: targetPush,
-            commitMessage: `move: ${finalNote.title}`,
+            commitMessage: targetCommitMessage,
             commitBody: targetCommitBody,
+            retry,
         }),
     };
 }
@@ -952,8 +988,21 @@ server.registerTool("set_project_identity", {
             `Resolved identity: ${candidateIdentity.project.id}\n` +
             `Remote: ${remoteName}`,
     });
-    await vaultManager.main.git.commit(`identity: ${defaultProject.name} use remote ${remoteName}`, ["config.json"], commitBody);
-    await pushAfterMutation(vaultManager.main);
+    const commitMessage = `identity: ${defaultProject.name} use remote ${remoteName}`;
+    const commitFiles = ["config.json"];
+    const commitStatus = await vaultManager.main.git.commitWithStatus(commitMessage, commitFiles, commitBody);
+    const pushStatus = commitStatus.status === "committed"
+        ? await pushAfterMutation(vaultManager.main)
+        : { status: "skipped", reason: "commit-failed" };
+    const retry = buildMutationRetryContract({
+        commit: commitStatus,
+        commitMessage,
+        commitBody,
+        files: commitFiles,
+        cwd,
+        vault: vaultManager.main,
+        mutationApplied: true,
+    });
     const structuredContent = {
         action: "project_identity_set",
         project: {
@@ -971,12 +1020,14 @@ server.registerTool("set_project_identity", {
             remoteName,
             updatedAt: now,
         },
+        retry,
     };
     return {
         content: [{
                 type: "text",
                 text: `Project identity override set for ${defaultProject.name}: ` +
-                    `default=\`${defaultProject.id}\`, effective=\`${candidateIdentity.project.id}\`, remote=${remoteName}`,
+                    `default=\`${defaultProject.id}\`, effective=\`${candidateIdentity.project.id}\`, remote=${remoteName}` +
+                    `${commitStatus.status === "failed" ? `\nCommit failed; retry data included. Push status: ${pushStatus.status}.` : ""}`,
             }],
         structuredContent,
     };
@@ -1236,16 +1287,30 @@ server.registerTool("remember", {
         scope: writeScope,
         tags: tags,
     });
-    const commitStatus = await vault.git.commitWithStatus(`remember: ${title}`, [vaultManager.noteRelPath(vault, id)], commitBody);
-    const pushStatus = await pushAfterMutation(vault);
+    const commitMessage = `remember: ${title}`;
+    const commitFiles = [vaultManager.noteRelPath(vault, id)];
+    const commitStatus = await vault.git.commitWithStatus(commitMessage, commitFiles, commitBody);
+    const pushStatus = commitStatus.status === "committed"
+        ? await pushAfterMutation(vault)
+        : { status: "skipped", reason: "commit-failed" };
+    const retry = buildMutationRetryContract({
+        commit: commitStatus,
+        commitMessage,
+        commitBody,
+        files: commitFiles,
+        cwd,
+        vault,
+        mutationApplied: true,
+    });
     const persistence = buildPersistenceStatus({
         storage: vault.storage,
         id,
         embedding: embeddingStatus,
         commit: commitStatus,
         push: pushStatus,
-        commitMessage: `remember: ${title}`,
+        commitMessage,
         commitBody,
+        retry,
     });
     const vaultLabel = vault.isProject ? " [project vault]" : " [main vault]";
     const textContent = `Remembered as \`${id}\` [${projectScope}, stored=${writeScope}]${vaultLabel}\n${formatPersistenceSummary(persistence)}`;
@@ -1345,8 +1410,21 @@ server.registerTool("set_project_memory_policy", {
                 ? `\nProtected branch patterns: ${effectiveProtectedBranchPatterns.join(", ")}`
                 : ""}`,
     });
-    await vaultManager.main.git.commit(`policy: ${project.name} default scope ${effectiveDefaultScope}`, ["config.json"], commitBody);
-    await pushAfterMutation(vaultManager.main);
+    const commitMessage = `policy: ${project.name} default scope ${effectiveDefaultScope}`;
+    const commitFiles = ["config.json"];
+    const commitStatus = await vaultManager.main.git.commitWithStatus(commitMessage, commitFiles, commitBody);
+    const pushStatus = commitStatus.status === "committed"
+        ? await pushAfterMutation(vaultManager.main)
+        : { status: "skipped", reason: "commit-failed" };
+    const retry = buildMutationRetryContract({
+        commit: commitStatus,
+        commitMessage,
+        commitBody,
+        files: commitFiles,
+        cwd,
+        vault: vaultManager.main,
+        mutationApplied: true,
+    });
     const structuredContent = {
         action: "policy_set",
         project: { id: project.id, name: project.name },
@@ -1354,13 +1432,15 @@ server.registerTool("set_project_memory_policy", {
         consolidationMode: effectiveConsolidationMode,
         protectedBranchBehavior: effectiveProtectedBranchBehavior,
         protectedBranchPatterns: effectiveProtectedBranchPatterns,
-        timestamp: now,
+        updatedAt: now,
+        retry,
     };
     return {
         content: [{
                 type: "text",
                 text: `Project memory policy set for ${project.name}: defaultScope=${effectiveDefaultScope}` +
-                    `${modeStr}${branchBehaviorStr}${branchPatternsStr}`,
+                    `${modeStr}${branchBehaviorStr}${branchPatternsStr}` +
+                    `${commitStatus.status === "failed" ? `\nCommit failed; retry data included. Push status: ${pushStatus.status}.` : ""}`,
             }],
         structuredContent,
     };
@@ -1473,6 +1553,20 @@ server.registerTool("recall", {
     const project = await resolveProject(cwd);
     const queryVec = await embed(query);
     const vaults = await vaultManager.searchOrder(cwd);
+    const noteCache = new Map();
+    const noteCacheKey = (vault, id) => `${vault.storage.vaultPath}::${id}`;
+    const readCachedNote = async (vault, id) => {
+        const key = noteCacheKey(vault, id);
+        const cached = noteCache.get(key);
+        if (cached) {
+            return cached;
+        }
+        const note = await vault.storage.readNote(id);
+        if (note) {
+            noteCache.set(key, note);
+        }
+        return note;
+    };
     for (const vault of vaults) {
         await embedMissingNotes(vault.storage).catch(() => { });
     }
@@ -1483,7 +1577,7 @@ server.registerTool("recall", {
             const rawScore = cosineSimilarity(queryVec, rec.embedding);
             if (rawScore < minSimilarity)
                 continue;
-            const note = await vault.storage.readNote(rec.id);
+            const note = await readCachedNote(vault, rec.id);
             if (!note)
                 continue;
             if (tags && tags.length > 0) {
@@ -1512,7 +1606,7 @@ server.registerTool("recall", {
     }
     const sections = [];
     for (const { id, score, vault } of top) {
-        const note = await vault.storage.readNote(id);
+        const note = await readCachedNote(vault, id);
         if (note)
             sections.push(formatNote(note, score));
     }
@@ -1523,7 +1617,7 @@ server.registerTool("recall", {
     // Build structured results array
     const structuredResults = [];
     for (const { id, score, vault, boosted } of top) {
-        const note = await vault.storage.readNote(id);
+        const note = await readCachedNote(vault, id);
         if (note) {
             structuredResults.push({
                 id,
@@ -1656,16 +1750,30 @@ server.registerTool("update", {
         projectName: updated.projectName,
         tags: updated.tags,
     });
-    const commitStatus = await vault.git.commitWithStatus(`update: ${updated.title}`, [vaultManager.noteRelPath(vault, id)], commitBody);
-    const pushStatus = await pushAfterMutation(vault);
+    const commitMessage = `update: ${updated.title}`;
+    const commitFiles = [vaultManager.noteRelPath(vault, id)];
+    const commitStatus = await vault.git.commitWithStatus(commitMessage, commitFiles, commitBody);
+    const pushStatus = commitStatus.status === "committed"
+        ? await pushAfterMutation(vault)
+        : { status: "skipped", reason: "commit-failed" };
+    const retry = buildMutationRetryContract({
+        commit: commitStatus,
+        commitMessage,
+        commitBody,
+        files: commitFiles,
+        cwd,
+        vault,
+        mutationApplied: true,
+    });
     const persistence = buildPersistenceStatus({
         storage: vault.storage,
         id,
         embedding: embeddingStatus,
         commit: commitStatus,
         push: pushStatus,
-        commitMessage: `update: ${updated.title}`,
+        commitMessage,
         commitBody,
+        retry,
     });
     const structuredContent = {
         action: "updated",
@@ -1745,6 +1853,7 @@ server.registerTool("forget", {
     const vaultChanges = await removeRelationshipsToNoteIds([id]);
     // Always include the deleted note's path (git add on a deleted file stages the removal)
     addVaultChange(vaultChanges, noteVault, vaultManager.noteRelPath(noteVault, id));
+    let retry;
     for (const [v, files] of vaultChanges) {
         const isPrimaryVault = v === noteVault;
         const summary = isPrimaryVault ? `Deleted note and cleaned up ${files.length - 1} reference(s)` : "Cleaned up dangling reference";
@@ -1754,8 +1863,22 @@ server.registerTool("forget", {
             noteTitle: note.title,
             projectName: note.projectName,
         });
-        await v.git.commit(`forget: ${note.title}`, files, commitBody);
-        await pushAfterMutation(v);
+        const commitMessage = `forget: ${note.title}`;
+        const commitStatus = await v.git.commitWithStatus(commitMessage, files, commitBody);
+        if (!retry) {
+            retry = buildMutationRetryContract({
+                commit: commitStatus,
+                commitMessage,
+                commitBody,
+                files,
+                cwd,
+                vault: v,
+                mutationApplied: true,
+            });
+        }
+        if (commitStatus.status === "committed") {
+            await pushAfterMutation(v);
+        }
     }
     const structuredContent = {
         action: "forgotten",
@@ -1765,6 +1888,7 @@ server.registerTool("forget", {
         projectName: note.projectName,
         relationshipsCleaned: vaultChanges.size > 0 ? Array.from(vaultChanges.values()).reduce((sum, files) => sum + files.length - 1, 0) : 0,
         vaultsModified: Array.from(vaultChanges.keys()).map(v => storageLabel(v)),
+        retry,
     };
     return { content: [{ type: "text", text: `Forgotten '${id}' (${note.title})` }], structuredContent };
 });
@@ -2432,7 +2556,7 @@ server.registerTool("move_memory", {
             updatedAt: new Date().toISOString(),
         };
     }
-    const moveResult = await moveNoteBetweenVaults(found, targetVault, noteToWrite);
+    const moveResult = await moveNoteBetweenVaults(found, targetVault, noteToWrite, cwd);
     const movedNote = moveResult.note;
     const associationValue = movedNote.projectName && movedNote.project
         ? `${movedNote.projectName} (${movedNote.project})`
@@ -2527,6 +2651,7 @@ server.registerTool("relate", {
         return { content: [{ type: "text", text: `Relationship already exists between '${fromId}' and '${toId}'` }], isError: true };
     }
     const modifiedNoteIds = [];
+    let retry;
     for (const [vault, files] of vaultChanges) {
         const isFromVault = vault === fromVault;
         const thisNote = isFromVault ? fromNote : toNote;
@@ -2541,8 +2666,22 @@ server.registerTool("relate", {
                 type,
             },
         });
-        await vault.git.commit(`relate: ${fromNote.title} ↔ ${toNote.title}`, files, commitBody);
-        await pushAfterMutation(vault);
+        const commitMessage = `relate: ${fromNote.title} ↔ ${toNote.title}`;
+        const commitStatus = await vault.git.commitWithStatus(commitMessage, files, commitBody);
+        if (!retry) {
+            retry = buildMutationRetryContract({
+                commit: commitStatus,
+                commitMessage,
+                commitBody,
+                files,
+                cwd,
+                vault,
+                mutationApplied: true,
+            });
+        }
+        if (commitStatus.status === "committed") {
+            await pushAfterMutation(vault);
+        }
         modifiedNoteIds.push(...files.map(f => path.basename(f, '.md')));
     }
     const dirStr = bidirectional ? "↔" : "→";
@@ -2553,6 +2692,7 @@ server.registerTool("relate", {
         type,
         bidirectional,
         notesModified: modifiedNoteIds,
+        retry,
     };
     return {
         content: [{ type: "text", text: `Linked \`${fromId}\` ${dirStr} \`${toId}\` (${type})` }],
@@ -2616,6 +2756,7 @@ server.registerTool("unrelate", {
     if (vaultChanges.size === 0) {
         return { content: [{ type: "text", text: `No relationship found between '${fromId}' and '${toId}'` }], isError: true };
     }
+    let retry;
     for (const [vault, files] of vaultChanges) {
         const found = foundFrom?.vault === vault ? foundFrom : foundTo;
         const commitBody = found
@@ -2625,8 +2766,22 @@ server.registerTool("unrelate", {
                 projectName: found.note.projectName,
             })
             : undefined;
-        await vault.git.commit(`unrelate: ${fromId} ↔ ${toId}`, files, commitBody);
-        await pushAfterMutation(vault);
+        const commitMessage = `unrelate: ${fromId} ↔ ${toId}`;
+        const commitStatus = await vault.git.commitWithStatus(commitMessage, files, commitBody);
+        if (!retry) {
+            retry = buildMutationRetryContract({
+                commit: commitStatus,
+                commitMessage,
+                commitBody,
+                files,
+                cwd,
+                vault,
+                mutationApplied: true,
+            });
+        }
+        if (commitStatus.status === "committed") {
+            await pushAfterMutation(vault);
+        }
     }
     const modifiedNoteIds = [];
     for (const [vault, files] of vaultChanges) {
@@ -2639,6 +2794,7 @@ server.registerTool("unrelate", {
         type: "related-to", // not tracked for unrelate
         bidirectional,
         notesModified: modifiedNoteIds,
+        retry,
     };
     return { content: [{ type: "text", text: `Removed relationship between \`${fromId}\` and \`${toId}\`` }], structuredContent };
 });
@@ -2751,21 +2907,22 @@ async function detectDuplicates(entries, threshold, project) {
     const checked = new Set();
     let foundCount = 0;
     const duplicates = [];
+    const embeddings = await loadEmbeddingsByNoteId(entries);
     for (let i = 0; i < entries.length; i++) {
         const entryA = entries[i];
         if (checked.has(entryA.note.id))
             continue;
-        const embeddingA = await entryA.vault.storage.readEmbedding(entryA.note.id);
+        const embeddingA = embeddings.get(entryA.note.id);
         if (!embeddingA)
             continue;
         for (let j = i + 1; j < entries.length; j++) {
             const entryB = entries[j];
             if (checked.has(entryB.note.id))
                 continue;
-            const embeddingB = await entryB.vault.storage.readEmbedding(entryB.note.id);
+            const embeddingB = embeddings.get(entryB.note.id);
             if (!embeddingB)
                 continue;
-            const similarity = cosineSimilarity(embeddingA.embedding, embeddingB.embedding);
+            const similarity = cosineSimilarity(embeddingA, embeddingB);
             if (similarity >= threshold) {
                 foundCount++;
                 lines.push(`${foundCount}. ${entryA.note.title} (${entryA.note.id})`);
@@ -2895,11 +3052,12 @@ async function suggestMerges(entries, threshold, defaultConsolidationMode, proje
     const checked = new Set();
     let suggestionCount = 0;
     const suggestions = [];
+    const embeddings = await loadEmbeddingsByNoteId(entries);
     for (let i = 0; i < entries.length; i++) {
         const entryA = entries[i];
         if (checked.has(entryA.note.id))
             continue;
-        const embeddingA = await entryA.vault.storage.readEmbedding(entryA.note.id);
+        const embeddingA = embeddings.get(entryA.note.id);
         if (!embeddingA)
             continue;
         const similar = [];
@@ -2907,10 +3065,10 @@ async function suggestMerges(entries, threshold, defaultConsolidationMode, proje
             const entryB = entries[j];
             if (checked.has(entryB.note.id))
                 continue;
-            const embeddingB = await entryB.vault.storage.readEmbedding(entryB.note.id);
+            const embeddingB = embeddings.get(entryB.note.id);
             if (!embeddingB)
                 continue;
-            const similarity = cosineSimilarity(embeddingA.embedding, embeddingB.embedding);
+            const similarity = cosineSimilarity(embeddingA, embeddingB);
             if (similarity >= threshold) {
                 similar.push({ entry: entryB, similarity });
             }
@@ -2972,6 +3130,16 @@ async function suggestMerges(entries, threshold, defaultConsolidationMode, proje
     };
     return { content: [{ type: "text", text: lines.join("\n") }], structuredContent };
 }
+async function loadEmbeddingsByNoteId(entries) {
+    const embeddings = new Map();
+    await Promise.all(entries.map(async (entry) => {
+        const record = await entry.vault.storage.readEmbedding(entry.note.id);
+        if (record) {
+            embeddings.set(entry.note.id, record.embedding);
+        }
+    }));
+    return embeddings;
+}
 async function executeMerge(entries, mergePlan, defaultConsolidationMode, project, cwd, explicitMode, policy, allowProtectedBranch = false) {
     const sourceIds = normalizeMergePlanSourceIds(mergePlan.sourceIds);
     const targetTitle = mergePlan.targetTitle.trim();
@@ -3162,6 +3330,7 @@ async function executeMerge(entries, mergePlan, defaultConsolidationMode, projec
     let targetPushStatus = { status: "skipped", reason: "no-remote" };
     let targetCommitBody;
     let targetCommitMessage;
+    let targetCommitFiles;
     for (const [vault, files] of vaultChanges) {
         const isTargetVault = vault === targetVault;
         // Determine action and summary based on mode
@@ -3199,14 +3368,28 @@ async function executeMerge(entries, mergePlan, defaultConsolidationMode, projec
             });
         const commitMessage = `${action}: ${targetTitle}`;
         const commitStatus = await vault.git.commitWithStatus(commitMessage, files, commitBody);
-        const pushStatus = await pushAfterMutation(vault);
+        const pushStatus = commitStatus.status === "committed"
+            ? await pushAfterMutation(vault)
+            : { status: "skipped", reason: "commit-failed" };
         if (isTargetVault) {
             targetCommitStatus = commitStatus;
             targetPushStatus = pushStatus;
             targetCommitBody = commitBody;
             targetCommitMessage = commitMessage;
+            targetCommitFiles = [...files];
         }
     }
+    const retry = targetCommitMessage && targetCommitFiles
+        ? buildMutationRetryContract({
+            commit: targetCommitStatus,
+            commitMessage: targetCommitMessage,
+            commitBody: targetCommitBody,
+            files: targetCommitFiles,
+            cwd,
+            vault: targetVault,
+            mutationApplied: true,
+        })
+        : undefined;
     const persistence = buildPersistenceStatus({
         storage: targetVault.storage,
         id: targetId,
@@ -3215,6 +3398,7 @@ async function executeMerge(entries, mergePlan, defaultConsolidationMode, projec
         push: targetPushStatus,
         commitMessage: targetCommitMessage,
         commitBody: targetCommitBody,
+        retry,
     });
     const lines = [];
     lines.push(`Consolidated ${sourceIds.length} notes into '${targetId}'`);
@@ -3245,6 +3429,7 @@ async function executeMerge(entries, mergePlan, defaultConsolidationMode, projec
         notesProcessed: entries.length,
         notesModified: vaultChanges.size,
         persistence,
+        retry,
     };
     return { content: [{ type: "text", text: lines.join("\n") }], structuredContent };
 }
@@ -3370,14 +3555,29 @@ async function pruneSuperseded(entries, consolidationMode, project, cwd, policy,
         }
     }
     // Commit changes per vault
+    let retry;
     for (const [vault, files] of vaultChanges) {
         const prunedIds = files.map((f) => f.replace(/\.mnemonic\/notes\/(.+)\.md$/, "$1").replace(/notes\/(.+)\.md$/, "$1"));
         const commitBody = formatCommitBody({
             noteIds: prunedIds,
             description: `Pruned ${prunedIds.length} superseded note(s)\nNotes: ${prunedIds.join(", ")}`,
         });
-        await vault.git.commit(`prune: removed ${files.length} superseded note(s)`, files, commitBody);
-        await pushAfterMutation(vault);
+        const commitMessage = `prune: removed ${files.length} superseded note(s)`;
+        const commitStatus = await vault.git.commitWithStatus(commitMessage, files, commitBody);
+        if (!retry) {
+            retry = buildMutationRetryContract({
+                commit: commitStatus,
+                commitMessage,
+                commitBody,
+                files,
+                cwd,
+                vault,
+                mutationApplied: true,
+            });
+        }
+        if (commitStatus.status === "committed") {
+            await pushAfterMutation(vault);
+        }
     }
     lines.push("");
     lines.push(`Pruned ${supersededIds.size} note(s).`);
@@ -3388,6 +3588,7 @@ async function pruneSuperseded(entries, consolidationMode, project, cwd, policy,
         projectName: project?.name,
         notesProcessed: entries.length,
         notesModified: vaultChanges.size,
+        retry,
     };
     return { content: [{ type: "text", text: lines.join("\n") }], structuredContent };
 }