gabriel / muse public
chore task/remove-stale-docs #1 / 1
AI Agent gabriel · 104 days ago · May 27, 2026 · Diff

chore: delete ported and stale docs

Remove files that have been ported to official /muse/* docs or are outdated: - WHITE_PAPER.md → ported to /muse/vision - guide/crdt-reference.md → ported to /muse/crdt - reference/security.md → ported to /muse/security - architecture/, demo/, protocol/ → stale planning/demo content - bridge-ci.md, crdt-midi-rga.md, crdt-music-rga.md → stale design notes - entity-identity.md, key-material-security-audit.md → stale audits - music-query-dsl.md, op-log.md, utility-reference.md → stale - guide/getting-started.md → superseded by /muse/getting-started (Phase 00) - reference/domains.md → superseded by /muse/domains (Phase 03) - reference/cli-tiers.md, reference/gc.md → internal

Remaining docs: agent-guide.md (load-bearing — referenced in global CLAUDE.md), plus reference docs for code-domain, midi-domain, auth, hub, remotes, and other features that warrant future official doc pages.

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Semantic Changes 983 symbols
− docs/architecture
− docs/demo
− docs/protocol
~ docs/README.md .md 14 symbols removed
− Muse Documentation section Muse Documentation L1–216
− Adding a New Domain section Adding a New Domain L176–188
− Architecture at a Glance section Architecture at a Glance L132–176
− code variable variable code L136–155
− table@L158 section table@L158 L158–166
− table@L169 section table@L169 L169–173
− Config Files Generated by muse init section Config Files Generated by muse init L188–200
− table section table L190–197
− Directory Map section Directory Map L41–132
− code variable variable code L43–129
− Quick Navigation section Quick Navigation L9–41
− table section table L11–38
− Testing Standards section Testing Standards L200–216
− code[bash] variable variable code[bash] L204–214
~ docs/WHITE_PAPER.md .md 23 symbols removed
− Muse: Domain Agnostic Version Control for Multi-Dimensional State section Muse: Domain Agnostic Version Control for Multi-Dimensional State L1–228
− A Concrete Example section A Concrete Example L62–90
− code@L72 variable variable code@L72 L72–75
− code@L80 variable variable code@L80 L80–83
− Entity Identity section Entity Identity L151–169
− code variable variable code L159–164
− Muse Today section Muse Today L181–191
− The Core Idea, Distilled section The Core Idea, Distilled L215–228
− The Domains Waiting section The Domains Waiting L191–205
− The Plugin Model: Teaching Muse New Domains section The Plugin Model: Teaching Muse New Domains L90–109
− The Problem in One Sentence section The Problem in One Sentence L11–17
− The World Git Was Built For Is Shrinking section The World Git Was Built For Is Shrinking L36–48
− What "Semantic Diff" Actually Feels Like section What "Semantic Diff" Actually Feels Like L109–151
− code@L113 variable variable code@L113 L113–116
− code@L119 variable variable code@L119 L119–123
− code@L126 variable variable code@L126 L126–129
− code@L132 variable variable code@L132 L132–136
− code@L141 variable variable code@L141 L141–146
− What Git Actually Does section What Git Actually Does L17–36
− code variable variable code L25–29
− What Muse Does Differently section What Muse Does Differently L48–62
− What Muse Is Not section What Muse Is Not L205–215
− Why This Matters for AI Agents Specifically section Why This Matters for AI Agents Specifically L169–181
~ docs/architecture/architecture-plan.md .md 97 symbols removed
− Muse — Architecture Plan: From File-Hash MVP to Universal Multidimensional VCS section Muse — Architecture Plan: From File-Hash MVP to Universal Multidimensional VCS L1–1392
− Honest Assessment of Current State section 1. Honest Assessment of Current State L22–56
− What is genuinely limited section What is genuinely limited L32–56
− code variable variable code L36–39
− table section table L44–51
− What is good and must be preserved section What is good and must be preserved L24–32
− North Star: What We're Building Toward section 2. North Star: What We're Building Toward L56–72
− Phase 1 — Typed Delta Algebra section 3. Phase 1 — Typed Delta Algebra L72–360
− 1 Motivation section 3.1 Motivation L78–84
− py section 3.2 New Type System in muse/domain.py L84–176
− code[python] variable variable code[python] L88–168
− 3 Updated Plugin Protocol section 3.3 Updated Plugin Protocol L176–213
− code[python]@L180 variable variable code[python]@L180 L180–198
− code[python]@L201 variable variable code[python]@L201 L201–212
− 4 Updated DriftReport section 3.4 Updated DriftReport L213–227
− code[python] variable variable code[python] L217–226
− 5 Updated MergeResult section 3.5 Updated MergeResult L227–245
− code[python] variable variable code[python] L231–244
− 6 Updated Music Plugin section 3.6 Updated Music Plugin L245–305
− code[python] variable variable code[python] L249–302
− 7 Serialisation Contract section 3.7 Serialisation Contract L305–311
− 8 Phase 1 Test Cases section 3.8 Phase 1 Test Cases L311–344
− code@L315 variable variable code@L315 L315–331
− code@L334 variable variable code@L334 L334–343
− 9 Files Changed in Phase 1 section 3.9 Files Changed in Phase 1 L344–360
− table section table L346–357
− Phase 2 — Domain Schema & Diff Algorithm Library section 4. Phase 2 — Domain Schema & Diff Algorithm Library L360–783
− 1 Motivation section 4.1 Motivation L366–372
− 2 Domain Schema Types section 4.2 Domain Schema Types L372–482
− code[python] variable variable code[python] L376–481
− 3 Schema Method Added to Plugin Protocol method section 4.3 Schema Method Added to Plugin Protocol L482–497
− code[python] variable variable code[python] L484–496
− 4 Example Schema Declarations section 4.4 Example Schema Declarations L497–631
− code[python]@L501 variable variable code[python]@L501 L501–563
− code[python]@L566 variable variable code[python]@L566 L566–628
− 5 Diff Algorithm Library section 4.5 Diff Algorithm Library L631–702
− code variable variable code L635–643
− code[python] variable variable code[python] L646–668
− 6 Plugin Registry Gains Schema Lookup section 4.6 Plugin Registry Gains Schema Lookup L702–706
− 7 Phase 2 Test Cases section 4.7 Phase 2 Test Cases L706–765
− code@L710 variable variable code@L710 L710–751
− code@L754 variable variable code@L754 L754–764
− 8 Files Changed in Phase 2 section 4.8 Files Changed in Phase 2 L765–783
− table section table L767–780
− Phase 3 — Operation-Level Merge Engine section 5. Phase 3 — Operation-Level Merge Engine L783–991
− 1 Motivation section 5.1 Motivation L789–795
− 2 Commutativity Rules section 5.2 Commutativity Rules L795–815
− table section table L799–812
− 3 Operation Transformer Functions function section 5.3 Operation Transformer Functions L815–875
− code[python] variable variable code[python] L819–874
− 4 Updated Core Merge Engine section 5.4 Updated Core Merge Engine L875–897
− code[python] variable variable code[python] L879–894
− 5 Plugin Protocol Gains merge_ops section 5.5 Plugin Protocol Gains merge_ops L897–923
− code[python] variable variable code[python] L901–922
− 6 Position Adjustment After Transform section 5.6 Position Adjustment After Transform L923–939
− code variable variable code L927–936
− 7 Phase 3 Test Cases section 5.7 Phase 3 Test Cases L939–978
− code variable variable code L943–977
− 8 Files Changed in Phase 3 section 5.8 Files Changed in Phase 3 L978–991
− table section table L980–988
− Phase 4 — CRDT Semantics for Convergent Multi-Agent Writes section 6. Phase 4 — CRDT Semantics for Convergent Multi-Agent Writes L991–1212
− 1 Motivation section 6.1 Motivation L997–1005
− 2 CRDT Primitive Library section 6.2 CRDT Primitive Library L1005–1081
− code variable variable code L1009–1019
− code[python]@L1024 variable variable code[python]@L1024 L1024–1039
− code[python]@L1048 variable variable code[python]@L1048 L1048–1064
− code[python]@L1069 variable variable code[python]@L1069 L1069–1080
− 3 CRDT-Aware Snapshot Format section 6.3 CRDT-Aware Snapshot Format L1081–1097
− code[python] variable variable code[python] L1085–1094
− 4 CRDTPlugin Protocol Extension section 6.4 CRDTPlugin Protocol Extension L1097–1137
− code[python] variable variable code[python] L1099–1136
− 5 When to Use CRDT Mode section 6.5 When to Use CRDT Mode L1137–1150
− table section table L1139–1147
− 6 Phase 4 Test Cases section 6.6 Phase 4 Test Cases L1150–1194
− code variable variable code L1154–1193
− 7 Files Changed in Phase 4 section 6.7 Files Changed in Phase 4 L1194–1212
− table section table L1196–1209
− Cross-Cutting Concerns section 7. Cross-Cutting Concerns L1212–1263
− 1 Content-Addressed Object Store Compatibility section 7.1 Content-Addressed Object Store Compatibility L1214–1222
− 2 Commit Record Format Evolution section 7.2 Commit Record Format Evolution L1222–1242
− code[python] variable variable code[python] L1226–1239
− 3 Wire Format for Agent-to-Agent Communication section 7.3 Wire Format for Agent-to-Agent Communication L1242–1246
− 4 Typing Constraints section 7.4 Typing Constraints L1246–1257
− 5 Synchronous I/O Constraint section 7.5 Synchronous I/O Constraint L1257–1263
− Test Strategy section 8. Test Strategy L1263–1311
− 1 Test Pyramid section 8.1 Test Pyramid L1265–1279
− code variable variable code L1267–1276
− 2 Property-Based Testing for Algorithms section 8.2 Property-Based Testing for Algorithms L1279–1296
− 3 Regression Test Naming Convention section 8.3 Regression Test Naming Convention L1296–1305
− code variable variable code L1299–1302
− 4 Test Isolation section 8.4 Test Isolation L1305–1311
− Implementation Order and Dependencies section 9. Implementation Order and Dependencies L1311–1392
− 1 Rough Timeline section 9.1 Rough Timeline L1346–1358
− table section table L1348–1355
− 2 Definition of Done Per Phase section 9.2 Definition of Done Per Phase L1358–1392
− code variable variable code L1313–1338
− Table of Contents section Table of Contents L8–22
~ docs/architecture/muse-e2e-demo.md .md 48 symbols removed
− Muse E2E Walkthrough section Muse E2E Walkthrough L1–295
− Full Summary Table section Full Summary Table L267–285
− table section table L269–282
− Setup section Setup L8–28
− code variable variable code L21–25
− code[bash] variable variable code[bash] L10–20
− Step 0 — Root Commit section Step 0 — Root Commit L28–55
− code@L35 variable variable code@L35 L35–38
− code@L43 variable variable code@L43 L43–52
− code[bash]@L30 variable variable code[bash]@L30 L30–34
− code[bash]@L39 variable variable code[bash]@L39 L39–42
− Step 1 — Mainline Commit section Step 1 — Mainline Commit L55–70
− code variable variable code L63–67
− code[bash] variable variable code[bash] L57–62
− Step 10 — Tag a Commit section Step 10 — Tag a Commit L254–267
− code variable variable code L261–264
− code[bash] variable variable code[bash] L256–260
− Step 2 — Branch A section Step 2 — Branch A L70–81
− code[bash] variable variable code[bash] L72–78
− Step 3 — Branch B (from Step 1) section Step 3 — Branch B (from Step 1) L81–106
− code variable variable code L96–103
− code[bash]@L83 variable variable code[bash]@L83 L83–91
− code[bash]@L92 variable variable code[bash]@L92 L92–95
− Step 4 — Clean Three-Way Merge section Step 4 — Clean Three-Way Merge L106–145
− code@L113 variable variable code@L113 L113–116
− code@L121 variable variable code@L121 L121–124
− code@L131 variable variable code@L131 L131–142
− code[bash]@L108 variable variable code[bash]@L108 L108–112
− code[bash]@L117 variable variable code[bash]@L117 L117–120
− code[bash]@L127 variable variable code[bash]@L127 L127–130
− Step 5 — Conflict Merge section Step 5 — Conflict Merge L145–188
− code@L169 variable variable code@L169 L169–174
− code@L182 variable variable code@L182 L182–185
− code[bash]@L149 variable variable code[bash]@L149 L149–168
− code[bash]@L175 variable variable code[bash]@L175 L175–181
− Step 6 — Cherry-Pick section Step 6 — Cherry-Pick L188–202
− code variable variable code L196–199
− code[bash] variable variable code[bash] L192–195
− Step 7 — Time-Travel Checkout section Step 7 — Time-Travel Checkout L202–223
− code variable variable code L212–215
− code[bash]@L204 variable variable code[bash]@L204 L204–211
− code[bash]@L216 variable variable code[bash]@L216 L216–220
− Step 8 — Revert section Step 8 — Revert L223–239
− code variable variable code L231–234
− code[bash] variable variable code[bash] L227–230
− Step 9 — Shelf and Restore section Step 9 — Shelf and Restore L239–254
− code[bash] variable variable code[bash] L243–251
− What This Proves section What This Proves L285–295
~ docs/architecture/muse-vcs.md .md 54 symbols removed
− Muse VCS — Architecture Reference section Muse VCS — Architecture Reference L1–524
− Adding a New Domain — Quick Reference section Adding a New Domain — Quick Reference L300–313
− CLI Command Reference section CLI Command Reference L313–430
− Low-level commands (top-level muse …) section Low-level commands (top-level muse …) L317–364
− table@L321 section table@L321 L321–335
− table@L338 section table@L338 L338–363
− Tier 3 — Semantic Porcelain section Tier 3 — Semantic Porcelain L364–430
− Code domain (muse code …) section Code domain (muse code …) L384–417
− table section table L386–416
− Coordination domain (muse coord …) section Coordination domain (muse coord …) L417–430
− table section table L419–427
− MIDI domain (muse midi …) section MIDI domain (muse midi …) L368–384
− table section table L370–383
− Core Engine Modules section Core Engine Modules L80–111
− code variable variable code L82–108
− Deterministic ID Derivation section Deterministic ID Derivation L111–126
− code variable variable code L115–120
− How CLI Commands Use the Plugin section How CLI Commands Use the Plugin L284–300
− table section table L286–297
− Key Design Decisions section Key Design Decisions L506–524
− Phase 1 — Typed Delta Algebra section Phase 1 — Typed Delta Algebra L126–148
− table section table L131–138
− Phase 2 — Domain Schema & Diff Algorithm Library section Phase 2 — Domain Schema & Diff Algorithm Library L148–167
− table section table L153–160
− Phase 3 — Operation-Level Merge Engine section Phase 3 — Operation-Level Merge Engine L167–208
− py) section Operational Transformation (muse/core/op_transform.py) L190–208
− table section table L192–198
− code[python] variable variable code[python] L171–185
− Phase 4 — CRDT Semantics section Phase 4 — CRDT Semantics L208–250
− CRDT Primitive Library (muse/core/crdts/) section CRDT Primitive Library (muse/core/crdts/) L224–238
− table section table L226–234
− When to use CRDT mode section When to use CRDT mode L238–250
− table section table L240–247
− code[python] variable variable code[python] L213–221
− Remote Sync section Remote Sync L430–489
− Commands section Commands L435–446
− table section table L437–445
− Local State for Remotes section Local State for Remotes L476–489
− code variable variable code L478–483
− MPack Wire Format section MPack Wire Format L462–476
− code variable variable code L470–475
− Transport Architecture section Transport Architecture L446–462
− code variable variable code L448–456
− Repository Structure on Disk section Repository Structure on Disk L47–80
− code variable variable code L51–74
− Testing & Verification section Testing & Verification L489–506
− code[bash] variable variable code[bash] L491–501
− The Full Plugin Protocol Stack section The Full Plugin Protocol Stack L250–284
− code variable variable code L252–270
− code[python] variable variable code[python] L273–281
− The Seven Invariants section The Seven Invariants L31–47
− code variable variable code L33–42
− What Muse Is section What Muse Is L8–31
− table section table L22–28
~ docs/bridge-ci.md .md 27 symbols removed
− muse bridge — CI Authentication & Usage section muse bridge — CI Authentication & Usage L1–214
− toml — Bridge State File section .muse/git-bridge.toml — Bridge State File L20–47
− Structure section Structure L31–47
− code[toml] variable variable code[toml] L33–46
− code variable variable code L26–30
− Attribution Map section Attribution Map L180–203
− code[bash] variable variable code[bash] L196–202
− code[json] variable variable code[json] L184–191
− CircleCI Example section CircleCI Example L144–180
− code[yaml] variable variable code[yaml] L146–179
− Environment Variables variable section Environment Variables L9–20
− table section table L11–19
− GitHub Actions Example section GitHub Actions Example L116–144
− code[yaml] variable variable code[yaml] L118–143
− Overview section Overview L3–9
− Security Notes section Security Notes L203–214
− Subcommand Reference section Subcommand Reference L47–116
− --watch mode section --watch mode L96–116
− code[bash] variable variable code[bash] L100–108
− code[json] variable variable code[json] L111–115
− muse bridge git-export section muse bridge git-export L62–75
− code[bash] variable variable code[bash] L66–74
− muse bridge git-import import section muse bridge git-import L49–62
− code[bash] variable variable code[bash] L53–61
− muse bridge git-status section muse bridge git-status L75–96
− code[bash] variable variable code[bash] L79–82
− code[json] variable variable code[json] L85–95
~ docs/crdt-midi-rga.md .md 13 symbols removed
− Voice-Aware Music RGA section Voice-Aware Music RGA L1–83
− CRDT laws section CRDT laws L38–48
− Music-RGA position key section Music-RGA position key L20–38
− code variable variable code L24–27
− table section table L28–34
− Related files section Related files L76–83
− table section table L78–83
− Relationship to the commit DAG section Relationship to the commit DAG L70–76
− Status section Status L3–12
− Tombstone semantics section Tombstone semantics L48–56
− Voice lane assignment section Voice lane assignment L56–70
− table section table L60–66
− Why standard RGA is wrong for music section Why standard RGA is wrong for music L12–20
~ docs/crdt-music-rga.md .md 13 symbols removed
− Voice-Aware Music RGA section Voice-Aware Music RGA L1–83
− CRDT laws section CRDT laws L38–48
− Music-RGA position key section Music-RGA position key L20–38
− code variable variable code L24–27
− table section table L28–34
− Related files section Related files L76–83
− table section table L78–83
− Relationship to the commit DAG section Relationship to the commit DAG L70–76
− Status section Status L3–12
− Tombstone semantics section Tombstone semantics L48–56
− Voice lane assignment section Voice lane assignment L56–70
− table section table L60–66
− Why standard RGA is wrong for music section Why standard RGA is wrong for music L12–20
~ docs/demo/README.md .md 11 symbols removed
− Muse — Demo Hub section Muse — Demo Hub L1–112
− Code Demo → section Code Demo → L37–64
− table section table L45–59
− MIDI Demo → section MIDI Demo → L11–37
− table section table L20–30
− Shared Architecture section Shared Architecture L64–99
− code@L68 variable variable code@L68 L68–74
− code@L77 variable variable code@L77 L77–83
− code@L86 variable variable code@L86 L86–92
− The Semantic Stack section The Semantic Stack L99–112
− table section table L101–108
~ docs/demo/demo-code.md .md 50 symbols removed
− Muse Code Plugin — Demo section Muse Code Plugin — Demo L1–480
− Act I — What's in the Snapshot? section Act I — What's in the Snapshot? L25–57
− muse code symbols — see every named thing section muse code symbols — see every named thing L27–57
− code variable variable code L29–49
− Act II — Grep the Symbol Graph section Act II — Grep the Symbol Graph L57–95
− muse code grep — semantic symbol search section muse code grep — semantic symbol search L59–95
− code@L61 variable variable code@L61 L61–69
− code@L70 variable variable code@L70 L70–77
− code@L78 variable variable code@L78 L78–86
− Act III — Query the Symbol Graph section Act III — Query the Symbol Graph L95–138
− muse code query — SQL for your codebase section muse code query — SQL for your codebase L97–138
− code@L108 variable variable code@L108 L108–117
− code@L118 variable variable code@L118 L118–126
− code@L99 variable variable code@L99 L99–107
− Act IV — Language Breakdown section Act IV — Language Breakdown L138–160
− muse code languages — composition at a glance section muse code languages — composition at a glance L140–160
− code variable variable code L142–154
− Act IX — Where is the Bedrock? section Act IX — Where is the Bedrock? L273–298
− muse code stable — symbol stability leaderboard section muse code stable — symbol stability leaderboard L275–298
− code variable variable code L277–290
− Act V — Who Changed What? section Act V — Who Changed What? L160–189
− muse code blame — per-symbol attribution section muse code blame — per-symbol attribution L162–189
− code variable variable code L164–180
− Act VI — Symbol History section Act VI — Symbol History L189–212
− muse code symbol-log — the life of a function function section muse code symbol-log — the life of a function L191–212
− code variable variable code L193–204
− Act VII — Detect Refactoring section Act VII — Detect Refactoring L212–238
− muse code detect-refactor — classify semantic changes class section muse code detect-refactor — classify semantic changes L214–238
− code variable variable code L216–229
− Act VIII — Where is the Instability? section Act VIII — Where is the Instability? L238–273
− muse code hotspots — symbol churn leaderboard section muse code hotspots — symbol churn leaderboard L240–273
− code variable variable code L242–256
− code[bash] variable variable code[bash] L262–266
− Act X — Hidden Dependencies section Act X — Hidden Dependencies L298–329
− muse code coupling — co-change analysis section muse code coupling — co-change analysis L300–329
− code variable variable code L302–315
− Act XI — Release Semantic Diff section Act XI — Release Semantic Diff L329–370
− muse code compare — any two historical snapshots section muse code compare — any two historical snapshots L331–370
− code variable variable code L333–359
− Act XII — The Agent Interface section Act XII — The Agent Interface L370–443
− muse code patch — surgical semantic modification section muse code patch — surgical semantic modification L372–443
− code[bash]@L376 variable variable code[bash]@L376 L376–389
− code[bash]@L398 variable variable code[bash]@L398 L398–408
− code[bash]@L411 variable variable code[bash]@L411 L411–427
− code[bash]@L435 variable variable code[bash]@L435 L435–438
− For AI Agents section For AI Agents L462–480
− Setup section Setup L14–25
− code[bash] variable variable code[bash] L16–22
− The Full Command Matrix section The Full Command Matrix L443–462
− table section table L445–459
~ docs/demo/demo-script.md .md 68 symbols removed
− 2) section Muse Demo — Video Narration Script (v0.1.2) L1–760
− ACT 1 — Foundation (Steps 1–5) section ACT 1 — Foundation (Steps 1–5) L64–105
− Step 1 — muse init section Step 1 — muse init L68–74
− Step 2 — muse commit -m "Root: initial state snapshot" section Step 2 — muse commit -m "Root: initial state snapshot" L74–85
− Step 3 — muse commit -m "Layer 1: add rhythmic dimension" section Step 3 — muse commit -m "Layer 1: add rhythmic dimension" L85–92
− Step 4 — muse commit -m "Layer 2: add harmonic dimension" section Step 4 — muse commit -m "Layer 2: add harmonic dimension" L92–98
− Step 5 — muse log --oneline section Step 5 — muse log --oneline L98–105
− ACT 2 — Divergence (Steps 6–16) section ACT 2 — Divergence (Steps 6–16) L105–152
− Step 16 — muse log --oneline section Step 16 — muse log --oneline L144–152
− Steps 12–15 — Branch gamma section Steps 12–15 — Branch gamma L136–144
− Steps 6–8 — Branch alpha section Steps 6–8 — Branch alpha L115–127
− Steps 9–11 — Branch beta section Steps 9–11 — Branch beta L127–136
− ACT 3 — Clean Merges (Steps 17–21) section ACT 3 — Clean Merges (Steps 17–21) L152–195
− Step 19 — muse status section Step 19 — muse status L166–170
− Step 20 — Merge beta → main section Step 20 — Merge beta → main L170–188
− Step 21 — muse log --oneline section Step 21 — muse log --oneline L188–195
− Steps 17–18 — Merge alpha → main section Steps 17–18 — Merge alpha → main L159–166
− ACT 4 — Conflict & Resolution (Steps 22–31) section ACT 4 — Conflict & Resolution (Steps 22–31) L195–276
− Step 29 — Merge conflict/right section Step 29 — Merge conflict/right L230–257
− code variable variable code L232–236
− Step 30 — Resolve and commit section Step 30 — Resolve and commit L257–267
− Step 31 — muse status section Step 31 — muse status L267–276
− Steps 22–23 — Branch conflict/left section Steps 22–23 — Branch conflict/left L205–213
− Steps 24–26 — Branch conflict/right section Steps 24–26 — Branch conflict/right L213–226
− Steps 27–28 — Merge conflict/left section Steps 27–28 — Merge conflict/left L226–230
− ACT 5 — Advanced Operations (Steps 32–41) section ACT 5 — Advanced Operations (Steps 32–41) L276–341
− Step 41 — muse log --stat section Step 41 — muse log --stat L331–341
− Steps 32–38 — The audition arc (pause here and explain this slowly) section Steps 32–38 — The audition arc (pause here and explain this slowly) L283–326
− 0 / muse tag list section Steps 39–40 — muse tag add release:v1.0 / muse tag list L326–331
− ACT 6 — Typed Delta Algebra (Steps 42–46) section ACT 6 — Typed Delta Algebra (Steps 42–46) L371–444
− Step 42 — muse read on a commit with note-level changes section Step 42 — muse read on a commit with note-level changes L383–412
− code variable variable code L385–396
− Step 43 — muse diff between two commits section Step 43 — muse diff between two commits L412–428
− code variable variable code L414–423
− Step 44 — muse log --stat section Step 44 — muse log --stat L428–444
− code variable variable code L432–438
− ACT 7 — Domain Schema & Diff Algorithms (Steps 47–51) section ACT 7 — Domain Schema & Diff Algorithms (Steps 47–51) L444–518
− Step 47 — muse domains section Step 47 — muse domains L448–481
− code variable variable code L450–476
− Step 48 — What the schema does section Step 48 — What the schema does L481–494
− Step 49 — muse domains --new genomics section Step 49 — muse domains --new genomics L494–518
− code variable variable code L496–507
− ACT 8 — Operation-Level OT Merge (Steps 52–56) section ACT 8 — Operation-Level OT Merge (Steps 52–56) L518–580
− Step 50 — Two branches, same file, different notes section Step 50 — Two branches, same file, different notes L525–540
− code variable variable code L527–531
− Step 51 — muse merge beta-notes with operation-level merge section Step 51 — muse merge beta-notes with operation-level merge L540–555
− code variable variable code L542–550
− Step 52 — When ops genuinely conflict section Step 52 — When ops genuinely conflict L555–580
− code@L557 variable variable code@L557 L557–561
− code@L566 variable variable code@L566 L566–571
− ACT 9 — CRDT Convergent Writes (Steps 57–61) section ACT 9 — CRDT Convergent Writes (Steps 57–61) L580–673
− Step 57 — CRDT mode: join always succeeds section Step 57 — CRDT mode: join always succeeds L595–603
− Step 58 — The six CRDT primitives section Step 58 — The six CRDT primitives L603–625
− code[python] variable variable code[python] L605–615
− Step 59 — ORSet: adds always win section Step 59 — ORSet: adds always win L625–641
− code[python] variable variable code[python] L627–636
− Step 60 — muse merge in CRDT mode section Step 60 — muse merge in CRDT mode L641–656
− code variable variable code L643–651
− three-way section Step 61 — When to use CRDT vs. three-way L656–673
− table section table L660–667
− APPENDIX — Speaker Notes section APPENDIX — Speaker Notes L712–760
− On questions you might get section On questions you might get L714–743
− Suggested chapter markers for YouTube section Suggested chapter markers for YouTube L743–760
− table section table L745–760
− DIMENSION MATRIX — Closing walkthrough (~60 s) section DIMENSION MATRIX — Closing walkthrough (~60 s) L341–371
− HEADER — Reading the stats (~20 s) section HEADER — Reading the stats (~20 s) L51–64
− INTRO — Before clicking anything (~90 s) section INTRO — Before clicking anything (~90 s) L18–51
− 0 (~60 s) section OUTRO — Muse v1.0 (~60 s) L673–712
~ docs/demo/midi-demo.md .md 116 symbols removed
− Muse MIDI Plugin — Demo section Muse MIDI Plugin — Demo L1–916
− Act I — What's in the Track? section Act I — What's in the Track? L28–66
− muse midi notes — musical notation view section muse midi notes — musical notation view L30–66
− code variable variable code L32–50
− code[bash] variable variable code[bash] L58–63
− Act II — See the Score section Act II — See the Score L66–95
− muse midi piano-roll — ASCII piano roll section muse midi piano-roll — ASCII piano roll L68–95
− code variable variable code L70–83
− code[bash] variable variable code[bash] L88–92
− Act III — The Harmonic Layer section Act III — The Harmonic Layer L95–137
− muse midi harmony — chord analysis and key detection section muse midi harmony — chord analysis and key detection L97–137
− code variable variable code L99–126
− Act IV — The Dynamic Layer section Act IV — The Dynamic Layer L137–174
− muse midi velocity-profile — dynamic range analysis section muse midi velocity-profile — dynamic range analysis L139–174
− code@L141 variable variable code@L141 L141–158
− code@L159 variable variable code@L159 L159–167
− Act IX — Agent Command: Mix section Act IX — Agent Command: Mix L317–357
− muse midi mix — layer two tracks into one section muse midi mix — layer two tracks into one L319–357
− code[bash]@L321 variable variable code[bash]@L321 L321–333
− code[bash]@L343 variable variable code[bash]@L343 L343–354
− Act V — Note-Level History section Act V — Note-Level History L174–209
− muse midi note-log — what changed in each commit section muse midi note-log — what changed in each commit L176–209
− code variable variable code L178–199
− Act VI — Note Attribution section Act VI — Note Attribution L209–240
− muse midi note-blame — which commit wrote these notes? section muse midi note-blame — which commit wrote these notes? L211–240
− code variable variable code L213–227
− Act VII — Where is the Compositional Instability? section Act VII — Where is the Compositional Instability? L240–270
− muse midi hotspots — bar-level churn section muse midi hotspots — bar-level churn L242–270
− code variable variable code L244–258
− code[bash] variable variable code[bash] L263–267
− Act VIII — Agent Command: Transpose section Act VIII — Agent Command: Transpose L270–317
− muse midi transpose — surgical pitch transformation section muse midi transpose — surgical pitch transformation L272–317
− code[bash]@L274 variable variable code[bash]@L274 L274–292
− code[bash]@L293 variable variable code[bash]@L293 L293–298
− code[bash]@L306 variable variable code[bash]@L306 L306–311
− Act X — Rhythmic Intelligence section Act X — Rhythmic Intelligence L357–415
− muse midi density — note density arc section muse midi density — note density arc L396–415
− code variable variable code L398–410
− muse midi rhythm — syncopation, swing, quantisation section muse midi rhythm — syncopation, swing, quantisation L359–381
− code variable variable code L361–371
− code[bash] variable variable code[bash] L374–378
− muse midi tempo — BPM estimation section muse midi tempo — BPM estimation L381–396
− code variable variable code L383–391
− Act XI — Pitch & Harmony (Deep) section Act XI — Pitch & Harmony (Deep) L415–494
− muse midi cadence — cadence detection section muse midi cadence — cadence detection L457–475
− code variable variable code L459–470
− muse midi contour — melodic contour section muse midi contour — melodic contour L475–494
− code variable variable code L477–489
− muse midi scale — scale and mode detection section muse midi scale — scale and mode detection L417–440
− code variable variable code L419–430
− code[bash] variable variable code[bash] L433–437
− muse midi tension — harmonic tension curve section muse midi tension — harmonic tension curve L440–457
− code variable variable code L442–452
− Act XII — Structure & Counterpoint section Act XII — Structure & Counterpoint L494–559
− muse midi instrumentation — channel & register map section muse midi instrumentation — channel & register map L540–559
− code variable variable code L542–554
− muse midi motif — recurring pattern detection section muse midi motif — recurring pattern detection L496–517
− code variable variable code L498–507
− code[bash] variable variable code[bash] L510–514
− muse midi voice-leading — counterpoint lint section muse midi voice-leading — counterpoint lint L517–540
− code variable variable code L519–530
− code[bash] variable variable code[bash] L533–537
− Act XIII — History Deep-Dive section Act XIII — History Deep-Dive L559–585
− muse midi compare — semantic diff between commits section muse midi compare — semantic diff between commits L561–585
− code variable variable code L563–580
− Act XIV — Multi-Agent Intelligence section Act XIV — Multi-Agent Intelligence L585–656
− muse midi agent-map — bar-level blame section muse midi agent-map — bar-level blame L587–612
− code variable variable code L589–602
− code[bash] variable variable code[bash] L605–609
− muse midi find-phrase — phrase similarity search section muse midi find-phrase — phrase similarity search L612–631
− code variable variable code L614–626
− muse midi shard — partition for parallel agents section muse midi shard — partition for parallel agents L631–656
− code variable variable code L633–646
− code[bash] variable variable code[bash] L649–653
− Act XV — Transformation Commands section Act XV — Transformation Commands L656–753
− muse midi arpeggiate — chords → arpeggios section muse midi arpeggiate — chords → arpeggios L724–738
− code[bash] variable variable code[bash] L726–733
− muse midi humanize — add human feel section muse midi humanize — add human feel L678–693
− code[bash] variable variable code[bash] L680–688
− muse midi invert — melodic inversion section muse midi invert — melodic inversion L693–709
− code[bash] variable variable code[bash] L695–704
− muse midi normalize — rescale velocities section muse midi normalize — rescale velocities L738–753
− code[bash] variable variable code[bash] L740–748
− muse midi quantize — snap to rhythmic grid section muse midi quantize — snap to rhythmic grid L658–678
− code[bash] variable variable code[bash] L660–672
− muse midi retrograde — play it backward section muse midi retrograde — play it backward L709–724
− code[bash] variable variable code[bash] L711–719
− For AI Agents Creating Music section For AI Agents Creating Music L886–916
− Setup section Setup L16–28
− code[bash] variable variable code[bash] L18–25
− The Full Collaborative Music Workflow section The Full Collaborative Music Workflow L753–806
− Agent B Adds Harmony section Agent B Adds Harmony L766–782
− code[bash] variable variable code[bash] L768–781
− Merge section Merge L782–794
− code[bash] variable variable code[bash] L784–793
− Quality Check section Quality Check L794–806
− code[bash] variable variable code[bash] L796–803
− Session Setup section Session Setup L757–766
− code[bash] variable variable code[bash] L759–765
− The Full Command Matrix — 31 Semantic Porcelain Commands section The Full Command Matrix — 31 Semantic Porcelain Commands L806–886
− History & Attribution section History & Attribution L843–851
− table section table L845–850
− Invariants & Quality Gates section Invariants & Quality Gates L873–886
− table section table L875–878
− Multi-Agent Intelligence section Multi-Agent Intelligence L851–860
− table section table L853–859
− Notation & Visualization section Notation & Visualization L808–816
− table section table L810–815
− Pitch, Harmony & Scale section Pitch, Harmony & Scale L816–826
− table section table L818–825
− Rhythm & Dynamics section Rhythm & Dynamics L826–835
− table section table L828–834
− Structure & Voice Leading section Structure & Voice Leading L835–843
− table section table L837–842
− Transformation section Transformation L860–873
− table section table L862–872
~ docs/entity-identity.md .md 13 symbols removed
− Entity Identity in Muse section Entity Identity in Muse L1–93
− Entity assignment heuristic section Entity assignment heuristic L30–42
− Entity index storage section Entity index storage L57–78
− code variable variable code L61–66
− code[toml] variable variable code[toml] L71–77
− Independence from core section Independence from core L78–85
− DeleteOp + InsertOp section MutateOp vs. DeleteOp + InsertOp L42–57
− table section table L46–53
− Related files section Related files L85–93
− table section table L87–93
− The problem with content hashes as identity section The problem with content hashes as identity L3–15
− The solution: stable entity IDs section The solution: stable entity IDs L15–30
− code variable variable code L22–29
~ docs/guide/crdt-reference.md .md 44 symbols removed
− Muse CRDT Reference section Muse CRDT Reference L1–476
− CRDTPlugin Integration section CRDTPlugin Integration L403–435
− code[python] variable variable code[python] L408–429
− Combining Primitives section Combining Primitives L374–403
− Example: a collaborative score header section Example: a collaborative score header L379–403
− code[python] variable variable code[python] L381–397
− Performance Notes section Performance Notes L435–454
− table section table L437–445
− Primitive Reference section Primitive Reference L90–374
− AWMap section AWMap L293–336
− API section API L303–336
− code[python] variable variable code[python] L305–333
− GCounter section GCounter L336–374
− API section API L347–374
− code[python] variable variable code[python] L349–371
− LWWRegister section LWWRegister L142–181
− API section API L153–174
− code[python] variable variable code[python] L155–173
− Warning on timestamps section Warning on timestamps L174–181
− ORSet section ORSet L181–235
− API section API L195–221
− code[python] variable variable code[python] L197–220
− Concurrent add + remove example section Concurrent add + remove example L221–235
− code variable variable code L223–232
− RGA section RGA L235–293
− API section API L246–275
− code[python] variable variable code[python] L248–274
− How concurrent insertions resolve section How concurrent insertions resolve L275–293
− code variable variable code L277–287
− VectorClock section VectorClock L103–142
− API section API L113–134
− code[python] variable variable code[python] L115–133
− When to use section When to use L134–142
− code[python] variable variable code[python] L94–97
− Table of Contents section Table of Contents L11–29
− The Three Lattice Laws section The Three Lattice Laws L53–90
− Commutativity section 1. Commutativity L59–68
− code variable variable code L61–64
− Associativity section 2. Associativity L68–77
− code variable variable code L70–73
− Idempotency section 3. Idempotency L77–90
− code variable variable code L79–82
− When Not to Use CRDTs section When Not to Use CRDTs L454–476
− Why CRDTs? section Why CRDTs? L29–53
~ docs/guide/getting-started.md .md 29 symbols removed
− Getting Started with Muse section Getting Started with Muse L1–204
− Dev Setup (contributors only) section Dev Setup (contributors only) L8–25
− code[bash] variable variable code[bash] L15–18
− Step 1 — Install section Step 1 — Install L25–64
− code[bash]@L32 variable variable code[bash]@L32 L32–35
− code[bash]@L38 variable variable code[bash]@L38 L38–42
− code[bash]@L45 variable variable code[bash]@L45 L45–50
− code[json] variable variable code[json] L53–57
− Step 2 — Uninstall (when needed) section Step 2 — Uninstall (when needed) L64–91
− code[bash]@L70 variable variable code[bash]@L70 L70–73
− code[bash]@L76 variable variable code[bash]@L76 L76–79
− code[bash]@L82 variable variable code[bash]@L82 L82–85
− Step 3 — Migrate an Existing Git Repository section Step 3 — Migrate an Existing Git Repository L91–181
− Add custom exclusion patterns section Add custom exclusion patterns L131–139
− code[bash] variable variable code[bash] L135–138
− Connect to MuseHub and push section Connect to MuseHub and push L159–181
− code[bash]@L163 variable variable code[bash]@L163 L163–171
− code[bash]@L175 variable variable code[bash]@L175 L175–178
− Incremental migration section Incremental migration L116–125
− code[bash] variable variable code[bash] L120–124
− JSON progress events (agents and CI) section JSON progress events (agents and CI) L139–159
− code variable variable code L144–152
− code[bash] variable variable code[bash] L155–158
− Migrate into a separate directory section Migrate into a separate directory L125–131
− code[bash] variable variable code[bash] L127–130
− Quick start section Quick start L96–116
− code[bash] variable variable code[bash] L98–115
− Step 4 — Learn the Full Muse Workflow section Step 4 — Learn the Full Muse Workflow L181–204
− table section table L197–202
~ docs/key-material-security-audit.md .md 49 symbols removed
− Key Material Security Audit — Muse + MuseHub section Key Material Security Audit — Muse + MuseHub L1–363
− Current State — What Exists Today section Current State — What Exists Today L32–92
− py section muse/cli/commands/auth.py L75–84
− py section muse/core/hdkeys.py L58–65
− py section muse/core/identity.py L41–51
− py section muse/core/keychain.py L34–41
− py section muse/core/keypair.py L51–58
− py section muse/core/msign.py L65–71
− py — SigningIdentity section muse/core/transport.py — SigningIdentity L71–75
− py section musehub/auth/request_signing.py L84–92
− Files to Delete (deferred cleanup) section Files to Delete (deferred cleanup) L346–363
− table section table L350–363
− Identified Issues (Ranked by Severity) section Identified Issues (Ranked by Severity) L92–132
− CRITICAL section CRITICAL L94–103
− table section table L96–102
− HIGH section HIGH L103–113
− table section table L105–112
− LOW section LOW L122–132
− table section table L124–129
− MEDIUM section MEDIUM L113–122
− table section table L115–121
− Implementation Plan section Implementation Plan L132–248
− Phase 1 — Fix the Mnemonic Keychain Key (C3) ✅ COMPLETE section Phase 1 — Fix the Mnemonic Keychain Key (C3) ✅ COMPLETE L134–145
− Phase 2 — Derive and Sign in Memory (C1, C2, H1) ✅ COMPLETE section Phase 2 — Derive and Sign in Memory (C1, C2, H1) ✅ COMPLETE L145–166
− code variable variable code L150–160
− toml Schema (C4) ⚠️ PARTIAL section Phase 3 — Remove key_path from identity.toml Schema (C4) ⚠️ PARTIAL L166–176
− py CLI Commands (H2, H4) ✅ COMPLETE section Phase 4 — Update auth.py CLI Commands (H2, H4) ✅ COMPLETE L176–187
− Phase 5 — Orphan PEM Cleanup ✅ COMPLETE section Phase 5 — Orphan PEM Cleanup ✅ COMPLETE L187–196
− Phase 6 — DerivedKey Zeroing Hardening (M1, M2) ✅ COMPLETE section Phase 6 — DerivedKey Zeroing Hardening (M1, M2) ✅ COMPLETE L196–225
− table section table L202–211
− Phase 7 — MuseHub Server Audit ✅ COMPLETE section Phase 7 — MuseHub Server Audit ✅ COMPLETE L225–236
− Phase 8 — Migrate run_recover and run_rotate off PEM files ✅ COMPLETE section Phase 8 — Migrate run_recover and run_rotate off PEM files ✅ COMPLETE L236–248
− Migration Path (Zero-Downtime) section Migration Path (Zero-Downtime) L260–270
− Post-Phase-8 Completeness Audit section Post-Phase-8 Completeness Audit L270–346
− Deleted functions — still referenced function section Deleted functions — still referenced L274–285
− table section table L276–284
− Docs and comments with stale key_path / PEM content section Docs and comments with stale key_path / PEM content L327–346
− table section table L329–343
− Test files calling deleted _key_path function function section Test files calling deleted _key_path function L297–303
− table section table L299–302
− Test files using key_path in identity entries (stale fixture data) section Test files using key_path in identity entries (stale fixture data) L314–327
− table section table L316–326
− key_path still in production code section key_path still in production code L285–297
− table section table L287–296
− key_set logic broken — 4 test failures section key_set logic broken — 4 test failures L303–314
− table section table L307–313
− Test Checklist section Test Checklist L248–260
− The Target Architecture section The Target Architecture L8–32
− code variable variable code L10–29
~ docs/music-query-dsl.md .md 14 symbols removed
− Music Query DSL section Music Query DSL L1–102
− Architecture section Architecture L70–84
− CLI flags section CLI flags L84–95
− code variable variable code L86–94
− Examples section Examples L51–70
− code[bash] variable variable code[bash] L53–69
− Grammar (EBNF) section Grammar (EBNF) L15–29
− code variable variable code L17–28
− Overview section Overview L3–15
− code[bash] variable variable code[bash] L8–14
− Related files section Related files L95–102
− table section table L97–102
− Supported fields section Supported fields L29–51
− table section table L31–46
~ docs/op-log.md .md 15 symbols removed
− Op Log: Append-Only Operation Log section Op Log: Append-Only Operation Log L1–91
− Checkpoints section Checkpoints L53–69
− code[python] variable variable code[python] L58–61
− Domain neutrality section Domain neutrality L78–84
− Lamport timestamps section Lamport timestamps L43–53
− Lifecycle section Lifecycle L69–78
− code variable variable code L71–77
− OpEntry fields section OpEntry fields L29–43
− table section table L31–42
− Purpose section Purpose L3–10
− Related files section Related files L84–91
− table section table L86–91
− Structure section Structure L21–29
− code variable variable code L23–28
− Why not just commit frequently? section Why not just commit frequently? L10–21
~ docs/protocol/muse-domain-concepts.md .md 16 symbols removed
− Muse Domain Concepts & Terminology section Muse Domain Concepts & Terminology L1–160
− Cross-Domain Term Mapping section Cross-Domain Term Mapping L90–111
− table section table L95–104
− Guidance for New Domain Authors section Guidance for New Domain Authors L141–160
− The Term "Variation" section The Term "Variation" L36–90
− Current meaning (MIDI domain) section Current meaning (MIDI domain) L42–67
− code variable variable code L48–51
− table section table L54–61
− Does it generalize? section Does it generalize? L67–90
− table section table L72–79
− Universal Terms (all domains, all plugins) section Universal Terms (all domains, all plugins) L9–36
− table section table L14–33
− What Is and Is Not Music-Specific section What Is and Is Not Music-Specific L111–141
− Definitely universal (core engine, all domains) section Definitely universal (core engine, all domains) L134–141
− MIDI-specific (stay in MIDI plugin only) section MIDI-specific (stay in MIDI plugin only) L113–125
− Potentially cross-domain (implemented for music, could generalize) section Potentially cross-domain (implemented for music, could generalize) L125–134
~ docs/protocol/muse-protocol.md .md 25 symbols removed
− MuseDomainPlugin Protocol — Language-Agnostic Specification section MuseDomainPlugin Protocol — Language-Agnostic Specification L1–392
− Purpose section 0. Purpose L8–20
− Design Principles section 1. Design Principles L20–38
− Type Definitions section 2. Type Definitions L38–76
− code[python] variable variable code[python] L43–73
− The Six Required Methods method section 3. The Six Required Methods L76–193
− 1 snapshot(live_state: LiveState) → StateSnapshot section 3.1 snapshot(live_state: LiveState) → StateSnapshot L78–94
− 2 diff(base: StateSnapshot, target: StateSnapshot, *, repo_root: Path | None = None) → StateDelta section 3.2 diff(base: StateSnapshot, target: StateSnapshot, *, repo_root: Path | None = None) → StateDelta L94–111
− 3 merge(base, left, right: StateSnapshot, *, repo_root: Path | None = None) → MergeResult section 3.3 merge(base, left, right: StateSnapshot, *, repo_root: Path | None = None) → MergeResult L111–140
− 4 drift(committed: StateSnapshot, live: LiveState) → DriftReport section 3.4 drift(committed: StateSnapshot, live: LiveState) → DriftReport L140–155
− 5 apply(delta: StateDelta, live_state: LiveState) → LiveState section 3.5 apply(delta: StateDelta, live_state: LiveState) → LiveState L155–174
− 6 schema() → DomainSchema section 3.6 schema() → DomainSchema L174–193
− Optional Protocol Extensions section 4. Optional Protocol Extensions L193–262
− 1 StructuredMergePlugin — Operational Transformation Merge section 4.1 StructuredMergePlugin — Operational Transformation Merge L195–228
− code[python] variable variable code[python] L199–212
− 2 CRDTPlugin — Convergent Multi-Agent Merge section 4.2 CRDTPlugin — Convergent Multi-Agent Merge L228–262
− code[python] variable variable code[python] L232–246
− Snapshot Format (Normative) section 5. Snapshot Format (Normative) L262–292
− code[json]@L266 variable variable code[json]@L266 L266–275
− code[json]@L278 variable variable code[json]@L278 L278–286
− Naming Conventions section 6. Naming Conventions L292–303
− table section table L294–300
− Implementing a Plugin section 7. Implementing a Plugin L303–379
− code[python] variable variable code[python] L307–371
− Invariants the Core Engine Relies On section 8. Invariants the Core Engine Relies On L379–392
~ docs/protocol/muse-variation-spec.md .md 30 symbols removed
− Muse Variation Spec — Music Domain Reference section Muse Variation Spec — Music Domain Reference L1–216
− API Endpoints section API Endpoints L158–181
− Commit request section Commit request L168–181
− code[json] variable variable code[json] L170–176
− table section table L160–167
− Audition Modes section Audition Modes L181–191
− table section table L183–188
− Data Shapes section Data Shapes L75–126
− NoteChange section NoteChange L103–126
− code[json] variable variable code[json] L105–118
− Phrase section Phrase L88–103
− code[json] variable variable code[json] L90–102
− Variation (meta event) section Variation (meta event) L77–88
− code[json] variable variable code[json] L79–87
− Execution Mode Policy section Execution Mode Policy L63–75
− table section table L65–70
− Lifecycle section Lifecycle L34–49
− code variable variable code L36–43
− Relationship to Muse VCS section Relationship to Muse VCS L201–216
− code variable variable code L209–212
− code[bash] variable variable code[bash] L205–208
− SSE Streaming Contract section SSE Streaming Contract L126–158
− code variable variable code L130–133
− code[json] variable variable code[json] L141–152
− table section table L134–139
− Safety Rules section Safety Rules L191–201
− Terminology section Terminology L49–63
− table section table L51–60
− What a Variation Is section What a Variation Is L12–34
− code variable variable code L18–26
~ docs/reference/cli-tiers.md .md 49 symbols removed
− Muse CLI — Three-Tier Architecture Reference section Muse CLI — Three-Tier Architecture Reference L1–410
− Extending with New Domains section Extending with New Domains L398–410
− Tier 1 — Low-level commands section Tier 1 — Low-level commands L24–233
− Commands section Commands L44–61
− table section table L46–60
− Contract section Contract L28–44
− JSON Output Schemas section JSON Output Schemas L61–233
− cat-object --format info section cat-object --format info L72–84
− code[json] variable variable code[json] L74–81
− commit-graph section commit-graph L171–193
− code[json] variable variable code[json] L173–192
− commit-tree section commit-tree L150–156
− code[json] variable variable code[json] L152–155
− hash-object section hash-object L63–72
− code[json] variable variable code[json] L65–71
− ls-files section ls-files L102–116
− code[json] variable variable code[json] L104–115
− ls-remote --json section ls-remote --json L217–233
− code[json] variable variable code[json] L219–230
− pack-objects / unpack-objects section pack-objects / unpack-objects L193–217
− code[json]@L197 variable variable code[json]@L197 L197–205
− code[json]@L208 variable variable code[json]@L208 L208–216
− read-commit section read-commit L116–136
− code[json] variable variable code[json] L121–135
− read-snapshot section read-snapshot L136–150
− code[json] variable variable code[json] L138–149
− rev-parse section rev-parse L84–102
− code[json]@L86 variable variable code[json]@L86 L86–92
− code[json]@L94 variable variable code[json]@L94 L94–101
− update-ref section update-ref L156–171
− code[json]@L158 variable variable code[json]@L158 L158–165
− code[json]@L167 variable variable code[json]@L167 L167–170
− Tier 2 — Core Porcelain section Tier 2 — Core Porcelain L233–268
− table section table L240–265
− Tier 3 — Semantic Porcelain section Tier 3 — Semantic Porcelain L268–398
− muse code … — Code Domain section muse code … — Code Domain L351–385
− table section table L353–384
− muse coord … — Multi-Agent Coordination section muse coord … — Multi-Agent Coordination L385–398
− table section table L387–395
− muse midi … — MIDI Domain section muse midi … — MIDI Domain L276–351
− table@L282 section table@L282 L282–287
− table@L290 section table@L290 L290–297
− table@L300 section table@L300 L300–306
− table@L309 section table@L309 L309–314
− table@L317 section table@L317 L317–322
− table@L325 section table@L325 L325–331
− table@L334 section table@L334 L334–344
− table@L347 section table@L347 L347–350
− code variable variable code L6–21
~ docs/reference/domains.md .md 41 symbols removed
− muse domains — Domain Plugin Dashboard & Marketplace Publisher section muse domains — Domain Plugin Dashboard & Marketplace Publisher L1–368
− Capability Levels section Capability Levels L152–169
− table section table L156–162
− Commands section Commands L44–152
− muse domains (dashboard) section muse domains (dashboard) L46–83
− code variable variable code L50–71
− table section table L77–80
− muse domains --new section muse domains --new L83–117
− code@L87 variable variable code@L87 L87–90
− code@L98 variable variable code@L98 L98–103
− table section table L106–114
− muse domains publish section muse domains publish L117–152
− code variable variable code L122–130
− table@L133 section table@L133 L133–140
− table@L143 section table@L143 L143–149
− Examples section Examples L290–368
− List all registered domains (machine-readable) section List all registered domains (machine-readable) L292–298
− code[bash] variable variable code[bash] L294–297
− Override capabilities for an out-of-repo publish section Override capabilities for an out-of-repo publish L320–342
− code[bash] variable variable code[bash] L322–341
− Scaffold and immediately publish a new domain section Scaffold and immediately publish a new domain L298–320
− code[bash] variable variable code[bash] L300–319
− Use via agent (musehub_publish_domain MCP tool) section Use via agent (musehub_publish_domain MCP tool) L342–368
− code[json] variable variable code[json] L347–365
− Overview section Overview L29–44
− code variable variable code L31–37
− Plugin Architecture section Plugin Architecture L252–290
− code variable variable code L257–269
− code[python] variable variable code[python] L277–287
− Publishing to MuseHub section Publishing to MuseHub L169–252
− Agent usage (--json) section Agent usage (--json) L226–252
− code[bash] variable variable code[bash] L228–236
− code[json] variable variable code[json] L239–246
− Authentication section Authentication L200–213
− code variable variable code L204–208
− Capabilities manifest section Capabilities manifest L171–200
− code[json] variable variable code[json] L188–199
− code[python] variable variable code[python] L176–184
− HTTP semantics section HTTP semantics L213–226
− table section table L218–225
− Table of Contents section Table of Contents L11–29
~ docs/reference/gc.md .md 16 symbols removed
− muse gc — garbage-collect unreachable objects section muse gc — garbage-collect unreachable objects L1–73
− Agent workflows section Agent workflows L57–67
− code[bash] variable variable code[bash] L59–66
− Exit codes section Exit codes L67–73
− table section table L69–73
− How it works section How it works L5–14
− Options section Options L22–29
− table section table L24–28
− Output section Output L29–41
− code@L31 variable variable code@L31 L31–34
− code@L37 variable variable code@L37 L37–40
− Safety guarantees section Safety guarantees L41–48
− Usage section Usage L14–22
− code[bash] variable variable code[bash] L16–21
− When to run section When to run L48–57
− table section table L50–56
~ docs/reference/security.md .md 57 symbols removed
− Security Architecture — Muse Trust Boundary Reference section Security Architecture — Muse Trust Boundary Reference L1–506
− Branch Name & Repo ID Validation section Branch Name & Repo ID Validation L135–169
− Branch name rules section Branch name rules L144–157
− table section table L146–156
− Where applied section Where applied L157–169
− Display Sanitization — ANSI Injection Defence section Display Sanitization — ANSI Injection Defence L218–263
− Characters stripped section Characters stripped L240–255
− table section table L242–252
− The attack section The attack L227–240
− code variable variable code L231–234
− Where applied section Where applied L255–263
− Glob Injection Prevention section Glob Injection Prevention L263–282
− code[python] variable variable code[python] L273–276
− HTTP Transport Hardening section HTTP Transport Hardening L348–384
− Content-Type guard section Content-Type guard L375–384
− HTTPS enforcement section HTTPS enforcement L362–368
− Redirect refusal section Redirect refusal L352–362
− Response size cap section Response size cap L368–375
− Identity Store Security section Identity Store Security L469–488
− table section table L476–485
− Local File Transport Hardening section Local File Transport Hardening L384–443
− Branch name validation section Branch name validation L404–418
− table section table L409–417
− Ref path containment section Ref path containment L418–433
− Symlink canonicalisation section Symlink canonicalisation L393–404
− Where applied section Where applied L433–443
− table section table L435–440
− Numeric Guards section Numeric Guards L282–306
− Where applied section Where applied L290–306
− table section table L292–303
− Object ID & Ref ID Validation section Object ID & Ref ID Validation L101–135
− Where applied section Where applied L121–135
− Why this matters section Why this matters L107–121
− code variable variable code L111–115
− Path Containment — Zip-Slip Defence section Path Containment — Zip-Slip Defence L169–218
− Symlink escape section Symlink escape L196–203
− The zip-slip attack section The zip-slip attack L177–196
− code[python]@L182 variable variable code[python]@L182 L182–186
− code[python]@L190 variable variable code[python]@L190 L190–195
− Where applied section Where applied L203–218
− Size Caps section Size Caps L488–506
− table section table L490–496
− Snapshot Integrity section Snapshot Integrity L443–469
− Null-byte separators in hash computation section Null-byte separators in hash computation L447–458
− Symlink and hidden-file exclusion section Symlink and hidden-file exclusion L458–469
− Table of Contents section Table of Contents L11–30
− Threat Model section Threat Model L30–47
− table section table L34–40
− Trust Boundary Design section Trust Boundary Design L47–77
− code variable variable code L51–66
− Validation Module section Validation Module L77–101
− code variable variable code L82–95
− XML Safety section XML Safety L306–348
− The attacks section The attacks L314–328
− code[xml] variable variable code[xml] L321–325
− Why a typed wrapper section Why a typed wrapper L328–348
− code[python] variable variable code[python] L336–345
~ docs/utility-reference.md .md 51 symbols removed
− Muse Utility Reference & Anti-Pattern Inventory section Muse Utility Reference & Anti-Pattern Inventory L1–402
− Anti-Pattern Inventory section Anti-Pattern Inventory L124–402
− Pattern 1 — Manual sha256: prefix construction section Pattern 1 — Manual sha256: prefix construction L126–160
− table section table L129–155
− Pattern 10 — Manual cryptographic prefix stripping / construction section Pattern 10 — Manual cryptographic prefix stripping / construction L359–369
− table section table L363–366
− Pattern 11 — --format flag instead of --json section Pattern 11 — --format flag instead of --json L369–402
− Known violations section Known violations L383–392
− table section table L385–391
− Legitimate --format uses (not violations) section Legitimate --format uses (not violations) L392–402
− table section table L394–400
− Pattern 2 — Manual prefix stripping outside the storage boundary section Pattern 2 — Manual prefix stripping outside the storage boundary L160–201
− Production code section Production code L165–181
− table section table L167–180
− Test code section Test code L181–201
− table section table L183–196
− sha256 for object IDs section Pattern 3 — Manual hashlib.sha256 for object IDs L201–214
− table section table L205–211
− Pattern 4 — Manual short ID truncation section Pattern 4 — Manual short ID truncation L214–257
− Production code section Production code L217–235
− table section table L223–232
− Test code (representative — use short_id consistently) section Test code (representative — use short_id consistently) L235–257
− table section table L237–254
− Pattern 5 — Manual UTC timestamp section Pattern 5 — Manual UTC timestamp L257–273
− table section table L260–270
− Pattern 6 — Manual JSON file loading section Pattern 6 — Manual JSON file loading L273–297
− Production code section Production code L276–287
− table section table L278–284
− Test code (representative sample) section Test code (representative sample) L287–297
− table section table L289–294
− uuid4() for content-addressed entity IDs section Pattern 7 — uuid.uuid4() for content-addressed entity IDs L297–331
− table section table L302–328
− Pattern 8 — Manual fake_id equivalent in tests section Pattern 8 — Manual fake_id equivalent in tests L331–342
− table section table L334–339
− Pattern 9 — Manual object path construction section Pattern 9 — Manual object path construction L342–359
− table section table L346–356
− ID Format Rules section ID Format Rules L72–91
− table section table L74–84
− The Storage-Boundary Rule section The Storage-Boundary Rule L91–124
− code variable variable code L99–106
− Utility Functions function section Utility Functions L10–72
− Focused modules — Path constructors section Focused modules — Path constructors L51–60
− table section table L53–59
− _types section muse.core._types L12–33
− _types — Object store layout constants variable section muse.core._types — Object store layout constants L33–42
− table section table L35–39
− table section table L14–32
− object_store — Object path utilities section muse.core.object_store — Object path utilities L42–51
− table section table L44–48
− validation — Input guards section muse.core.validation — Input guards L60–72
− table section table L62–69
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