@markjaquith/agency 1.5.2 → 1.6.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@markjaquith/agency",
-  "version": "1.5.2",
+  "version": "1.6.0",
   "description": "Manages personal agents files",
   "license": "MIT",
   "author": "Mark Jaquith",
@@ -45,21 +45,21 @@
     "personal-agents"
   ],
   "devDependencies": {
-    "@types/bun": "latest",
-    "knip": "^5.70.1",
-    "prettier": "^3.6.2"
+    "@types/bun": "^1.3.6",
+    "knip": "^5.82.1",
+    "prettier": "^3.8.1"
   },
   "peerDependencies": {
-    "typescript": "^5"
+    "typescript": "^5.9.3"
   },
   "engines": {
     "bun": ">=1.0.0"
   },
   "dependencies": {
     "@effect/schema": "^0.75.5",
-    "effect": "^3.19.6",
+    "effect": "^3.19.15",
     "jsonc-parser": "^3.3.1",
-    "ora": "^8.1.1"
+    "ora": "^8.2.0"
   },
   "trustedDependencies": [
     "@triggi/native-exec"

package/src/commands/emit.integration.test.ts

@@ -224,7 +224,7 @@ describe("emit command - integration tests (requires git-filter-repo)", () => {
 		// Create a new feature branch
 		await createBranch(tempDir, "agency/claude-test")
 
-		// Initialize agency on this branch (this will modify CLAUDE.md)
+		// Initialize agency on this branch - first commit has agency files (NOT including CLAUDE.md)
 		await Bun.write(
 			join(tempDir, "agency.json"),
 			JSON.stringify({
@@ -235,22 +235,27 @@ describe("emit command - integration tests (requires git-filter-repo)", () => {
 			}),
 		)
 		await Bun.write(join(tempDir, "AGENTS.md"), "# Test AGENTS\n")
+		await addAndCommit(
+			tempDir,
+			"agency.json AGENTS.md",
+			"Initialize agency files",
+		)
 
-		// Simulate what agency task does - inject into CLAUDE.md
+		// Simulate what agency task now does - CLAUDE.md modification in a separate commit
+		// with AGENCY_REMOVE_COMMIT marker so the commit gets dropped during emit
 		const originalClaude = await Bun.file(join(tempDir, "CLAUDE.md")).text()
 		const modifiedClaude = `${originalClaude}\n# Agency References\n@AGENTS.md\n@TASK.md\n`
 		await Bun.write(join(tempDir, "CLAUDE.md"), modifiedClaude)
-
 		await addAndCommit(
 			tempDir,
-			"agency.json AGENTS.md CLAUDE.md",
-			"Initialize agency files",
+			"CLAUDE.md",
+			"chore: agency edit CLAUDE.md\n\nAGENCY_REMOVE_COMMIT",
 		)
 
 		// Add a feature file
 		await createCommit(tempDir, "Feature commit")
 
-		// Create emit branch (this should filter CLAUDE.md)
+		// Create emit branch (this should drop the CLAUDE.md modification commit)
 		await runTestEffect(emit({ silent: true, baseBranch: "main" }))
 
 		// Should still be on source branch
@@ -274,4 +279,271 @@ describe("emit command - integration tests (requires git-filter-repo)", () => {
 		expect(claudeContent).not.toContain("@AGENTS.md")
 		expect(claudeContent).not.toContain("@TASK.md")
 	})
+
+	describe("AGENCY_REMOVE_COMMIT edge cases", () => {
+		test("handles two contiguous AGENCY_REMOVE_COMMIT commits", async () => {
+			if (!hasGitFilterRepo) {
+				console.log("Skipping test: git-filter-repo not installed")
+				return
+			}
+
+			await checkoutBranch(tempDir, "main")
+
+			// Create two files on main that will be modified
+			await Bun.write(join(tempDir, "FILE1.md"), "Original content 1\n")
+			await Bun.write(join(tempDir, "FILE2.md"), "Original content 2\n")
+			await addAndCommit(tempDir, "FILE1.md FILE2.md", "Add files")
+
+			await createBranch(tempDir, "agency/contiguous-test")
+
+			// Create agency.json
+			await Bun.write(
+				join(tempDir, "agency.json"),
+				JSON.stringify({
+					version: 1,
+					injectedFiles: [],
+					template: "test",
+					createdAt: new Date().toISOString(),
+				}),
+			)
+			await addAndCommit(tempDir, "agency.json", "Add agency.json")
+
+			// Two contiguous AGENCY_REMOVE_COMMIT commits
+			await Bun.write(join(tempDir, "FILE1.md"), "Modified content 1\n")
+			await addAndCommit(
+				tempDir,
+				"FILE1.md",
+				"chore: edit FILE1\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			await Bun.write(join(tempDir, "FILE2.md"), "Modified content 2\n")
+			await addAndCommit(
+				tempDir,
+				"FILE2.md",
+				"chore: edit FILE2\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			// Add a feature commit after
+			await createCommit(tempDir, "Feature commit")
+
+			await runTestEffect(emit({ silent: true, baseBranch: "main" }))
+			await checkoutBranch(tempDir, "contiguous-test")
+
+			// Both files should be reverted to original
+			const file1 = await Bun.file(join(tempDir, "FILE1.md")).text()
+			const file2 = await Bun.file(join(tempDir, "FILE2.md")).text()
+			expect(file1).toBe("Original content 1\n")
+			expect(file2).toBe("Original content 2\n")
+
+			// Feature commit should still exist
+			const files = await getGitOutput(tempDir, ["ls-files"])
+			expect(files).toContain("test.txt")
+		})
+
+		test("handles two non-contiguous AGENCY_REMOVE_COMMIT commits", async () => {
+			if (!hasGitFilterRepo) {
+				console.log("Skipping test: git-filter-repo not installed")
+				return
+			}
+
+			await checkoutBranch(tempDir, "main")
+
+			await Bun.write(join(tempDir, "FILE1.md"), "Original content 1\n")
+			await Bun.write(join(tempDir, "FILE2.md"), "Original content 2\n")
+			await addAndCommit(tempDir, "FILE1.md FILE2.md", "Add files")
+
+			await createBranch(tempDir, "agency/non-contiguous-test")
+
+			await Bun.write(
+				join(tempDir, "agency.json"),
+				JSON.stringify({
+					version: 1,
+					injectedFiles: [],
+					template: "test",
+					createdAt: new Date().toISOString(),
+				}),
+			)
+			await addAndCommit(tempDir, "agency.json", "Add agency.json")
+
+			// First AGENCY_REMOVE_COMMIT
+			await Bun.write(join(tempDir, "FILE1.md"), "Modified content 1\n")
+			await addAndCommit(
+				tempDir,
+				"FILE1.md",
+				"chore: edit FILE1\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			// Regular commit in between
+			await Bun.write(join(tempDir, "feature1.txt"), "feature 1\n")
+			await addAndCommit(tempDir, "feature1.txt", "Add feature 1")
+
+			// Second AGENCY_REMOVE_COMMIT
+			await Bun.write(join(tempDir, "FILE2.md"), "Modified content 2\n")
+			await addAndCommit(
+				tempDir,
+				"FILE2.md",
+				"chore: edit FILE2\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			// Another regular commit
+			await Bun.write(join(tempDir, "feature2.txt"), "feature 2\n")
+			await addAndCommit(tempDir, "feature2.txt", "Add feature 2")
+
+			await runTestEffect(emit({ silent: true, baseBranch: "main" }))
+			await checkoutBranch(tempDir, "non-contiguous-test")
+
+			// Both files should be reverted to original
+			const file1 = await Bun.file(join(tempDir, "FILE1.md")).text()
+			const file2 = await Bun.file(join(tempDir, "FILE2.md")).text()
+			expect(file1).toBe("Original content 1\n")
+			expect(file2).toBe("Original content 2\n")
+
+			// Feature commits should still exist
+			const files = await getGitOutput(tempDir, ["ls-files"])
+			expect(files).toContain("feature1.txt")
+			expect(files).toContain("feature2.txt")
+		})
+
+		test("handles AGENCY_REMOVE_COMMIT as first commit after fork point", async () => {
+			if (!hasGitFilterRepo) {
+				console.log("Skipping test: git-filter-repo not installed")
+				return
+			}
+
+			await checkoutBranch(tempDir, "main")
+
+			await Bun.write(join(tempDir, "EXISTING.md"), "Original content\n")
+			await addAndCommit(tempDir, "EXISTING.md", "Add existing file")
+
+			await createBranch(tempDir, "agency/first-commit-test")
+
+			// First commit is AGENCY_REMOVE_COMMIT (modifying existing file)
+			await Bun.write(join(tempDir, "EXISTING.md"), "Modified content\n")
+			await addAndCommit(
+				tempDir,
+				"EXISTING.md",
+				"chore: edit EXISTING\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			// Then agency.json
+			await Bun.write(
+				join(tempDir, "agency.json"),
+				JSON.stringify({
+					version: 1,
+					injectedFiles: [],
+					template: "test",
+					createdAt: new Date().toISOString(),
+				}),
+			)
+			await addAndCommit(tempDir, "agency.json", "Add agency.json")
+
+			// Feature commit
+			await createCommit(tempDir, "Feature commit")
+
+			await runTestEffect(emit({ silent: true, baseBranch: "main" }))
+			await checkoutBranch(tempDir, "first-commit-test")
+
+			// File should be reverted to original
+			const content = await Bun.file(join(tempDir, "EXISTING.md")).text()
+			expect(content).toBe("Original content\n")
+
+			// Feature commit should exist
+			const files = await getGitOutput(tempDir, ["ls-files"])
+			expect(files).toContain("test.txt")
+		})
+
+		test("handles AGENCY_REMOVE_COMMIT as last commit", async () => {
+			if (!hasGitFilterRepo) {
+				console.log("Skipping test: git-filter-repo not installed")
+				return
+			}
+
+			await checkoutBranch(tempDir, "main")
+
+			await Bun.write(join(tempDir, "EXISTING.md"), "Original content\n")
+			await addAndCommit(tempDir, "EXISTING.md", "Add existing file")
+
+			await createBranch(tempDir, "agency/last-commit-test")
+
+			// agency.json first
+			await Bun.write(
+				join(tempDir, "agency.json"),
+				JSON.stringify({
+					version: 1,
+					injectedFiles: [],
+					template: "test",
+					createdAt: new Date().toISOString(),
+				}),
+			)
+			await addAndCommit(tempDir, "agency.json", "Add agency.json")
+
+			// Feature commit
+			await Bun.write(join(tempDir, "feature.txt"), "feature\n")
+			await addAndCommit(tempDir, "feature.txt", "Add feature")
+
+			// Last commit is AGENCY_REMOVE_COMMIT
+			await Bun.write(join(tempDir, "EXISTING.md"), "Modified content\n")
+			await addAndCommit(
+				tempDir,
+				"EXISTING.md",
+				"chore: edit EXISTING\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			await runTestEffect(emit({ silent: true, baseBranch: "main" }))
+			await checkoutBranch(tempDir, "last-commit-test")
+
+			// File should be reverted to original
+			const content = await Bun.file(join(tempDir, "EXISTING.md")).text()
+			expect(content).toBe("Original content\n")
+
+			// Feature commit should exist
+			const files = await getGitOutput(tempDir, ["ls-files"])
+			expect(files).toContain("feature.txt")
+		})
+
+		test("handles AGENCY_REMOVE_COMMIT as only commit (besides agency.json)", async () => {
+			if (!hasGitFilterRepo) {
+				console.log("Skipping test: git-filter-repo not installed")
+				return
+			}
+
+			await checkoutBranch(tempDir, "main")
+
+			await Bun.write(join(tempDir, "EXISTING.md"), "Original content\n")
+			await addAndCommit(tempDir, "EXISTING.md", "Add existing file")
+
+			await createBranch(tempDir, "agency/only-commit-test")
+
+			// agency.json
+			await Bun.write(
+				join(tempDir, "agency.json"),
+				JSON.stringify({
+					version: 1,
+					injectedFiles: [],
+					template: "test",
+					createdAt: new Date().toISOString(),
+				}),
+			)
+			await addAndCommit(tempDir, "agency.json", "Add agency.json")
+
+			// Only other commit is AGENCY_REMOVE_COMMIT
+			await Bun.write(join(tempDir, "EXISTING.md"), "Modified content\n")
+			await addAndCommit(
+				tempDir,
+				"EXISTING.md",
+				"chore: edit EXISTING\n\nAGENCY_REMOVE_COMMIT",
+			)
+
+			await runTestEffect(emit({ silent: true, baseBranch: "main" }))
+			await checkoutBranch(tempDir, "only-commit-test")
+
+			// File should be reverted to original
+			const content = await Bun.file(join(tempDir, "EXISTING.md")).text()
+			expect(content).toBe("Original content\n")
+
+			// Emit branch should exist and have the file
+			const files = await getGitOutput(tempDir, ["ls-files"])
+			expect(files).toContain("EXISTING.md")
+		})
+	})
 })

package/src/commands/emit.test.ts

@@ -305,12 +305,13 @@ describe("emit command", () => {
 			const lastCall = getLastCapturedFilterRepoCall()
 			expect(lastCall).toBeDefined()
 
-			// Should include paths for base files (TASK.md, AGENCY.md, CLAUDE.md, agency.json)
+			// Should include paths for base files (TASK.md, AGENCY.md, agency.json)
+			// Note: CLAUDE.md is NOT in base files - it's only filtered if it was created
+			// by agency (in which case it would be in injectedFiles)
 			// and injected files (AGENTS.md)
 			expect(lastCall!.args).toContain("--path")
 			expect(lastCall!.args).toContain("TASK.md")
 			expect(lastCall!.args).toContain("AGENCY.md")
-			expect(lastCall!.args).toContain("CLAUDE.md")
 			expect(lastCall!.args).toContain("agency.json")
 			expect(lastCall!.args).toContain("AGENTS.md")
 
@@ -336,12 +337,12 @@ describe("emit command", () => {
 			// Create CLAUDE.md as a symlink to AGENTS.md
 			await symlink("AGENTS.md", join(tempDir, "CLAUDE.md"))
 
-			// Create agency.json
+			// Create agency.json with CLAUDE.md in injectedFiles (since it's no longer in baseFiles)
 			await Bun.write(
 				join(tempDir, "agency.json"),
 				JSON.stringify({
 					version: 1,
-					injectedFiles: [],
+					injectedFiles: ["CLAUDE.md"],
 					template: "test",
 					createdAt: new Date().toISOString(),
 				}),

package/src/commands/emit.ts

@@ -197,10 +197,17 @@ const emitCore = (gitRoot: string, options: EmitOptions) =>
 			})
 			verboseLog(`Files to filter: ${filesToFilter.join(", ")}`)
 
-			// Run git-filter-repo
+			// Run git-filter-repo with:
+			// 1. Path filtering to remove backpack files
+			// 2. Commit callback to drop file changes from commits marked with AGENCY_REMOVE_COMMIT
+			//    (clearing file_changes makes the commit empty and it gets pruned, while preserving tree state)
 			const filterRepoArgs = [
 				...filesToFilter.flatMap((f) => ["--path", f]),
 				"--invert-paths",
+				"--commit-callback",
+				// Clear file changes from commits with AGENCY_REMOVE_COMMIT marker
+				// This makes the commit empty (which gets pruned) while preserving the tree state
+				`if b"AGENCY_REMOVE_COMMIT" in commit.message: commit.file_changes = []`,
 				"--force",
 				"--refs",
 				`${forkPoint}..${emitBranchName}`,

package/src/commands/task.ts

@@ -731,12 +731,18 @@ export const task = (options: TaskOptions = {}) =>
 		}
 
 		// Handle CLAUDE.md injection
+		// If CLAUDE.md is created (new file), include it in main commit and add to injectedFiles
+		// If CLAUDE.md is modified (existing file), commit separately with AGENCY_REMOVE_COMMIT marker
+		// so it can be completely removed during emission
 		const claudeResult = yield* claudeService.injectAgencySection(targetPath)
+		let claudeModifiedExisting = false
 		if (claudeResult.created) {
 			createdFiles.push("CLAUDE.md")
+			injectedFiles.push("CLAUDE.md")
 			log(done(`Created ${highlight.file("CLAUDE.md")}`))
 		} else if (claudeResult.modified) {
-			createdFiles.push("CLAUDE.md")
+			// Mark that we need a separate commit for CLAUDE.md modification
+			claudeModifiedExisting = true
 			log(done(`Updated ${highlight.file("CLAUDE.md")}`))
 		}
 
@@ -814,6 +820,27 @@ export const task = (options: TaskOptions = {}) =>
 				}),
 			)
 		}
+
+		// Create separate commit for CLAUDE.md modification with AGENCY_REMOVE_COMMIT marker
+		// This commit will be completely removed during emission
+		if (claudeModifiedExisting) {
+			yield* Effect.gen(function* () {
+				yield* git.gitAdd(["CLAUDE.md"], targetPath)
+				// The AGENCY_REMOVE_COMMIT marker in the commit body tells emit to drop this commit entirely
+				const commitMessage = `chore: agency edit CLAUDE.md\n\nAGENCY_REMOVE_COMMIT`
+				yield* git.gitCommit(commitMessage, targetPath, {
+					noVerify: true,
+				})
+				verboseLog(
+					"Created CLAUDE.md modification commit (will be removed on emit)",
+				)
+			}).pipe(
+				Effect.catchAll((err) => {
+					verboseLog(`Failed to commit CLAUDE.md modification: ${err}`)
+					return Effect.void
+				}),
+			)
+		}
 	})
 
 // Helper: Create feature branch with interactive prompts

package/src/services/AgencyMetadataService.ts

@@ -49,7 +49,7 @@ export class AgencyMetadataService extends Context.Tag("AgencyMetadataService")<
 
 		/**
 		 * Get list of files to filter during PR/merge operations.
-		 * Always includes TASK.md, AGENCY.md, CLAUDE.md, and agency.json, plus any injectedFiles from metadata.
+		 * Always includes TASK.md, AGENCY.md, and agency.json, plus any injectedFiles from metadata.
 		 */
 		readonly getFilesToFilter: (
 			gitRoot: string,
@@ -204,7 +204,7 @@ export const AgencyMetadataServiceLive = Layer.succeed(
 				const metadataPath = join(gitRoot, "agency.json")
 
 				const exists = yield* fs.exists(metadataPath)
-				const baseFiles = ["TASK.md", "AGENCY.md", "CLAUDE.md", "agency.json"]
+				const baseFiles = ["TASK.md", "AGENCY.md", "agency.json"]
 
 				if (!exists) {
 					// Resolve symlinks even for base files
@@ -236,7 +236,7 @@ export const AgencyMetadataServiceLive = Layer.succeed(
 				return yield* resolveSymlinkTargets(fs, gitRoot, expandedFiles)
 			}).pipe(
 				Effect.catchAll(() =>
-					Effect.succeed(["TASK.md", "AGENCY.md", "CLAUDE.md", "agency.json"]),
+					Effect.succeed(["TASK.md", "AGENCY.md", "agency.json"]),
 				),
 			),
 

package/src/utils/process.ts

@@ -23,7 +23,7 @@ interface SpawnOptions {
 /**
  * Generic error for process execution failures
  */
-export class ProcessError extends Data.TaggedError("ProcessError")<{
+class ProcessError extends Data.TaggedError("ProcessError")<{
 	command: string
 	exitCode: number
 	stderr: string