TODO inventory: migrate remaining ~570 TODOs to GitHub issues

[friedenberg]

Context

A systematic inventory of all TODO comments in the Go codebase was performed on 2026-03-21 (branch quiet-baobab). The goal is to reduce TODO debt by either fixing items directly or lifting them into tracked GitHub issues.

Work completed

Issues created

• Remove encoding/gob dependency entirely #26 — Remove gob serialization support (5 TODOs removed, code preserved for migration)
• ADR: panic/cancellation vs error-return semantics #27 — ADR: panic/cancellation vs error-return semantics (8 TODOs across 8 files linked)
• Generalize tag collection helpers into generic collection utilities #28 — Generalize tag collection helpers in bravo/ids (5 TODOs linked)
• Add shell completion for blob store IDs #29 — Implement blob store fsck/completion commands (3 TODOs linked)
• Move sorted collection helpers from quiter to collections_slice #30 — Move sorted helpers from quiter to collections_slice (3 TODOs linked)
• doddish scanner: modernize error handling and operator model #31 — Doddish scanner: modernize error handling and operator model (6 TODOs linked)

Direct fixes

• blech32 error types — Replaced 6 fmt.Errorf calls with typed errors (ErrInvalidChecksum, ErrMixedCase, errInvalidHRPCharacter, errDataPortionTooShort)
• blob_store_configs rename — TomlV{0,1,2} → TomlLocalHashBucketedV{0,1,2} (7 files)
• markl errLength — Added missing Is() (with marker interface for generics) and GetErrorType() methods
• markl errWrongHasher — New error type for hash algorithm mismatches
• gob TODOs — Removed 5 TODO comments after creating Remove encoding/gob dependency entirely #26

TODO format convention

All linked TODOs use a two-line format:

// TODO https://github.com/amarbel-llc/dodder/issues/N
// Cleaned-up description of what needs to happen

Remaining inventory (~570 TODOs, 19 clusters)

Cluster	Count	Notes
Refactoring / Code Structure / Rename	57	Package splits, moves, renames. Includes env_dir split (4 TODOs), organize_text refactors, command pattern migrations
Organize / Edit / Checkout / Merge	45	merge.go has 12 TODOs alone. organize_text constructor duplicated (constructor.go / constructor2.go)
Performance / Memory / Pooling	39	Pool additions, repool fixes, cache additions, read-and-discard → os.Stat
Remote / Network / HTTP / SFTP	38	SFTP config, HTTP server/client improvements, remote_transfer hacks
Interface / Type Design	38	domain_interfaces markl redesign (4 TODOs), object_id3 fields, commit_options methods, sku types
Store / Config Architecture	37	env_workspace bootstrap, store_config compiled splits, env_dir constants
Format / Serialization / Encoding	36	markl binary coding, hyphence improvements, box_format parser, stream_index
JSON / Lua / MCP Scripting	27	sku_json_fmt duplicated across hotel/india, lua_transacted field TODOs
CLI Commands / Completion / UI	27	Completion refactoring (duplicated dodder/madder), info command renames
Filesystem / Directory / File I/O	24	blob_mover splits (4 TODOs), dir_info improvements, store_fs
Object Commit / Mutation / Locking	20	mutating.go has 12 TODOs, finalizer options
Query Engine	19	build_state decision tree, executor refactoring, sigil/digest support
Error Handling	18	Missing error contexts, deferred error capture, box_format parse errors
IDs / ZettelId	18	Tai pointer issue, zettel_id doddish.Seq migration, hash format hardcoding
Cryptography / Security / Signing	17	InsecureIgnoreHostKey (2), signing middleware extraction, TOFU prompt
Tags / Types / Genres	14	Type package split, deprecated type removal, bookmark type migration
Miscellaneous	12	Scattered single TODOs
Tests / Test Infrastructure	6	test_ui migration, scanner_test framework
Inventory Lists / Coders	5	SeqCoder error support, repool fixes

How to resume

1. Pick a cluster from the table above
2. Read the relevant files to understand the TODOs in context
3. For each TODO, decide: fix directly (if simple) or create a GitHub issue
4. If creating an issue, update the TODO to the two-line format with full URL
5. Commit in logical batches (one commit per cluster or sub-cluster)

High-value clusters to tackle next

• Error Handling (18) — Many are simple "add context" or "capture error" fixes
• CLI Commands / Completion (27) — The info-* renames and completion duplications are straightforward
• Tags / Types / Genres (14) — Small cluster, likely quick to triage
• Tests / Test Infrastructure (6) — Smallest cluster, easy wins