Update .gitignore, add CLI cheatsheet, and modify benchmark results

- Updated .gitignore to include new target files and reports.
- Added a new CLI cheatsheet document for quick reference on commands and flags.
- Modified benchmark results in `bench/dirty-vs-full.md` to reflect updated performance metrics.
- Changed permissions for `run_all_tests.sh` to make it executable.
- Updated `target/.rustc_info.json` with additional output information.
- Adjusted file modes for `target/release/marlin` and `target/release/marlin.d`.

.gitignore

@@ -48,3 +48,7 @@ saved_config.yaml
 /target/
 /cobertura.xml
 /tarpaulin-report.html
+target/.rustc_info.json
+target/release/marlin
+target/release/marlin.d
+tarpaulin-report.html

bench/dirty-vs-full.md

@@ -1,4 +1,4 @@
 | Command | Mean [ms] | Min [ms] | Max [ms] | Relative |
 |:---|---:|---:|---:|---:|
-| `full-scan` | 504.7 ± 38.5 | 462.3 | 562.2 | 6.75 ± 0.67 |
-| `dirty-scan` | 74.8 ± 4.8 | 66.9 | 81.3 | 1.00 |
+| `full-scan` | 631.7 ± 78.1 | 541.8 | 711.3 | 8.72 ± 1.39 |
+| `dirty-scan` | 72.5 ± 7.3 | 63.2 | 85.7 | 1.00 |

cli-bin/docs/cli_cheatsheet.md

@@ -0,0 +1,23 @@
+| Command | Flags |
+| ------- | ----- |
+| `link add` | --type |
+| `link rm` | --type |
+| `link list` | --direction, --type |
+| `link backlinks` | — |
+| `coll create` | — |
+| `coll add` | — |
+| `coll list` | — |
+| `view save` | — |
+| `view list` | — |
+| `view exec` | — |
+| `state set` | — |
+| `state transitions-add` | — |
+| `state log` | — |
+| `task scan` | — |
+| `task list` | --due-today |
+| `remind set` | — |
+| `annotate add` | --range, --highlight |
+| `annotate list` | — |
+| `version diff` | — |
+| `event add` | — |
+| `event timeline` | — |

target/.rustc_info.json

@@ -1 +1 @@
-{"rustc_fingerprint":490527502257410439,"outputs":{"17747080675513052775":{"success":true,"status":"","code":0,"stdout":"rustc 1.87.0 (17067e9ac 2025-05-09)\nbinary: rustc\ncommit-hash: 17067e9ac6d7ecb70e50f92c1944e545188d2359\ncommit-date: 2025-05-09\nhost: x86_64-unknown-linux-gnu\nrelease: 1.87.0\nLLVM version: 20.1.1\n","stderr":""}},"successes":{}}
+{"rustc_fingerprint":490527502257410439,"outputs":{"17747080675513052775":{"success":true,"status":"","code":0,"stdout":"rustc 1.87.0 (17067e9ac 2025-05-09)\nbinary: rustc\ncommit-hash: 17067e9ac6d7ecb70e50f92c1944e545188d2359\ncommit-date: 2025-05-09\nhost: x86_64-unknown-linux-gnu\nrelease: 1.87.0\nLLVM version: 20.1.1\n","stderr":""},"7971740275564407648":{"success":true,"status":"","code":0,"stdout":"___\nlib___.rlib\nlib___.so\nlib___.so\nlib___.a\nlib___.so\n/home/user/.rustup/toolchains/stable-x86_64-unknown-linux-gnu\noff\npacked\nunpacked\n___\ndebug_assertions\npanic=\"unwind\"\nproc_macro\ntarget_abi=\"\"\ntarget_arch=\"x86_64\"\ntarget_endian=\"little\"\ntarget_env=\"gnu\"\ntarget_family=\"unix\"\ntarget_feature=\"fxsr\"\ntarget_feature=\"sse\"\ntarget_feature=\"sse2\"\ntarget_has_atomic=\"16\"\ntarget_has_atomic=\"32\"\ntarget_has_atomic=\"64\"\ntarget_has_atomic=\"8\"\ntarget_has_atomic=\"ptr\"\ntarget_os=\"linux\"\ntarget_pointer_width=\"64\"\ntarget_vendor=\"unknown\"\nunix\n","stderr":""},"10431901537437931773":{"success":true,"status":"","code":0,"stdout":"___\nlib___.rlib\nlib___.so\nlib___.so\nlib___.a\nlib___.so\n/home/user/.rustup/toolchains/stable-x86_64-unknown-linux-gnu\noff\npacked\nunpacked\n___\ndebug_assertions\npanic=\"unwind\"\nproc_macro\ntarget_abi=\"\"\ntarget_arch=\"x86_64\"\ntarget_endian=\"little\"\ntarget_env=\"gnu\"\ntarget_family=\"unix\"\ntarget_feature=\"fxsr\"\ntarget_feature=\"sse\"\ntarget_feature=\"sse2\"\ntarget_has_atomic=\"16\"\ntarget_has_atomic=\"32\"\ntarget_has_atomic=\"64\"\ntarget_has_atomic=\"8\"\ntarget_has_atomic=\"ptr\"\ntarget_os=\"linux\"\ntarget_pointer_width=\"64\"\ntarget_vendor=\"unknown\"\ntarpaulin\nunix\n","stderr":""}},"successes":{}}

target/release/marlin.d

@@ -1 +1 @@
-/workspace/Marlin/target/release/marlin: /workspace/Marlin/cli-bin/build.rs /workspace/Marlin/cli-bin/src/cli/annotate.rs /workspace/Marlin/cli-bin/src/cli/coll.rs /workspace/Marlin/cli-bin/src/cli/event.rs /workspace/Marlin/cli-bin/src/cli/link.rs /workspace/Marlin/cli-bin/src/cli/remind.rs /workspace/Marlin/cli-bin/src/cli/state.rs /workspace/Marlin/cli-bin/src/cli/task.rs /workspace/Marlin/cli-bin/src/cli/version.rs /workspace/Marlin/cli-bin/src/cli/view.rs /workspace/Marlin/cli-bin/src/cli/watch.rs /workspace/Marlin/cli-bin/src/cli.rs /workspace/Marlin/cli-bin/src/main.rs /workspace/Marlin/libmarlin/src/backup.rs /workspace/Marlin/libmarlin/src/config.rs /workspace/Marlin/libmarlin/src/db/database.rs /workspace/Marlin/libmarlin/src/db/migrations/0001_initial_schema.sql /workspace/Marlin/libmarlin/src/db/migrations/0002_update_fts_and_triggers.sql /workspace/Marlin/libmarlin/src/db/migrations/0003_create_links_collections_views.sql /workspace/Marlin/libmarlin/src/db/migrations/0004_fix_hierarchical_tags_fts.sql /workspace/Marlin/libmarlin/src/db/migrations/0005_add_dirty_table.sql /workspace/Marlin/libmarlin/src/db/mod.rs /workspace/Marlin/libmarlin/src/error.rs /workspace/Marlin/libmarlin/src/lib.rs /workspace/Marlin/libmarlin/src/logging.rs /workspace/Marlin/libmarlin/src/scan.rs /workspace/Marlin/libmarlin/src/utils.rs /workspace/Marlin/libmarlin/src/watcher.rs
+/home/user/Documents/GitHub/Marlin/target/release/marlin: /home/user/Documents/GitHub/Marlin/cli-bin/build.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/annotate.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/coll.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/commands.yaml /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/event.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/link.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/remind.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/state.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/task.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/version.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/view.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli/watch.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/cli.rs /home/user/Documents/GitHub/Marlin/cli-bin/src/main.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/backup.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/config.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/db/database.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0001_initial_schema.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0002_update_fts_and_triggers.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0003_create_links_collections_views.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0004_fix_hierarchical_tags_fts.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/migrations/0005_add_dirty_table.sql /home/user/Documents/GitHub/Marlin/libmarlin/src/db/mod.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/error.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/lib.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/logging.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/scan.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/utils.rs /home/user/Documents/GitHub/Marlin/libmarlin/src/watcher.rs