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openkb remove leaves orphan hash and reformats unrelated wiki #58

Closed
#62
Closed
openkb remove leaves orphan hash and reformats unrelated wiki#58
#62

Description

@wooogy-dev
wooogy-dev
opened on May 18, 2026

A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
they share a single repro, but they have different root causes and need separate fixes.

Follow-up to #41 — both are regressions in the implementation shipped by PR #51.

Repro

  1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
    wikilinks.
  2. openkb remove <that-doc> (e.g. openkb remove ollama).
  3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.

Bug 1 — hash entry is not removed for docs ingested before PR #51

cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.

Root cause

Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
into the registry. However, entries that already existed in hashes.json before that commit were not
backfilled — they still carry only {name, type}.

HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
False. The method silently returns False; nothing in the call chain checks the return value.

Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
is invisible at the surface.

Suggested fix

Either of the following — both are robust against un-backfilled legacy data:

  • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
  • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
    matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
    presence.

A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
but the call-site fix above is sufficient and avoids touching user data on read paths.

Bug 2 — unrelated wiki pages get reformatted

Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.

Example (from a concept page unrelated to ollama):

- **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki

Root cause

cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
get swept up too.

Impact

  • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
  • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
  • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
    refactoring.

Suggested fix (preferred)

Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
{index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
without sweeping the rest of the KB.

Alternatives

  • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
  • Make the global pass opt-in via a flag (e.g. --lint), default off.

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openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
      Skip to content
      openkb remove leaves orphan hash and reformats unrelated wiki #58
      Closed
      #62
      Closed
      openkb remove leaves orphan hash and reformats unrelated wiki#58
      #62
      Description
      @wooogy-dev
      wooogy-dev
      opened on May 18, 2026
      A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
      
they share a single repro, but they have different root causes and need separate fixes.
      Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
      Repro
      1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
        
wikilinks.
      2. openkb remove <that-doc> (e.g. openkb remove ollama).
      3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
      Bug 1 — hash entry is not removed for docs ingested before PR #51
      cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
      
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
      Root cause
      Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
      
into the registry. However, entries that already existed in hashes.json before that commit were not
      
backfilled       — they still carry only {name, type}.
      HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
      False. The method silently returns False; nothing in the call chain checks the return value.
      Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
      
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
      
is invisible at the surface.
      Suggested fix
      Either of the following — both are robust against un-backfilled legacy data:
      • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
      • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
        
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
        
presence.
      A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
      
but the call-site fix above is sufficient and avoids touching user data on read paths.
      Bug 2 — unrelated wiki pages get reformatted
      Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
      39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
      Example (from a concept page unrelated to ollama):
      - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
      Root cause
      cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
      openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
      
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
      
get swept up too.
      Impact
      • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
      • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
      • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
        
refactoring.
      Suggested fix (preferred)
      Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
      {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
      
without sweeping the rest of the KB.
      Alternatives
      • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
      • Make the global pass opt-in via a flag (e.g. --lint), default off.
      Metadata
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          No branches or pull requests
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openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
          Skip to content
          openkb remove leaves orphan hash and reformats unrelated wiki #58
          Closed
          #62
          Closed
          openkb remove leaves orphan hash and reformats unrelated wiki#58
          #62
          Description
          @wooogy-dev
          wooogy-dev
          opened on May 18, 2026
          A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
          
they share a single repro, but they have different root causes and need separate fixes.
          Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
          Repro
          1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
            
wikilinks.
          2. openkb remove <that-doc> (e.g. openkb remove ollama).
          3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
          Bug 1 — hash entry is not removed for docs ingested before PR #51
          cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
          
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
          Root cause
          Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
          
into the registry. However, entries that already existed in hashes.json before that commit were not
          
backfilled           — they still carry only {name, type}.
          HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
          False. The method silently returns False; nothing in the call chain checks the return value.
          Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
          
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
          
is invisible at the surface.
          Suggested fix
          Either of the following — both are robust against un-backfilled legacy data:
          • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
          • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
            
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
            
presence.
          A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
          
but the call-site fix above is sufficient and avoids touching user data on read paths.
          Bug 2 — unrelated wiki pages get reformatted
          Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
          39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
          Example (from a concept page unrelated to ollama):
          - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
          Root cause
          cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
          openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
          
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
          
get swept up too.
          Impact
          • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
          • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
          • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
            
refactoring.
          Suggested fix (preferred)
          Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
          {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
          
without sweeping the rest of the KB.
          Alternatives
          • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
          • Make the global pass opt-in via a flag (e.g. --lint), default off.
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            No labels
            No labels
            Type
            No type
            Projects
            No projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, 'i');
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var __re = new RegExp('^' + ".*" + '
openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
              Skip to content
              openkb remove leaves orphan hash and reformats unrelated wiki #58
              Closed
              #62
              Closed
              openkb remove leaves orphan hash and reformats unrelated wiki#58
              #62
              Description
              @wooogy-dev
              wooogy-dev
              opened on May 18, 2026
              A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
              
they share a single repro, but they have different root causes and need separate fixes.
              Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
              Repro
              1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
                
wikilinks.
              2. openkb remove <that-doc> (e.g. openkb remove ollama).
              3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
              Bug 1 — hash entry is not removed for docs ingested before PR #51
              cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
              
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
              Root cause
              Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
              
into the registry. However, entries that already existed in hashes.json before that commit were not
              
backfilled               — they still carry only {name, type}.
              HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
              False. The method silently returns False; nothing in the call chain checks the return value.
              Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
              
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
              
is invisible at the surface.
              Suggested fix
              Either of the following — both are robust against un-backfilled legacy data:
              • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
              • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
                
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
                
presence.
              A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
              
but the call-site fix above is sufficient and avoids touching user data on read paths.
              Bug 2 — unrelated wiki pages get reformatted
              Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
              39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
              Example (from a concept page unrelated to ollama):
              - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
              Root cause
              cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
              openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
              
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
              
get swept up too.
              Impact
              • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
              • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
              • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
                
refactoring.
              Suggested fix (preferred)
              Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
              {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
              
without sweeping the rest of the KB.
              Alternatives
              • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
              • Make the global pass opt-in via a flag (e.g. --lint), default off.
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                No labels
                No labels
                Type
                No type
                Projects
                No projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions
                  
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var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
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var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
                  Skip to content
                  openkb remove leaves orphan hash and reformats unrelated wiki #58
                  Closed
                  #62
                  Closed
                  openkb remove leaves orphan hash and reformats unrelated wiki#58
                  #62
                  Description
                  @wooogy-dev
                  wooogy-dev
                  opened on May 18, 2026
                  A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
                  
they share a single repro, but they have different root causes and need separate fixes.
                  Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
                  Repro
                  1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
                    
wikilinks.
                  2. openkb remove <that-doc> (e.g. openkb remove ollama).
                  3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
                  Bug 1 — hash entry is not removed for docs ingested before PR #51
                  cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
                  
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
                  Root cause
                  Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
                  
into the registry. However, entries that already existed in hashes.json before that commit were not
                  
backfilled                   — they still carry only {name, type}.
                  HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
                  False. The method silently returns False; nothing in the call chain checks the return value.
                  Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
                  
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
                  
is invisible at the surface.
                  Suggested fix
                  Either of the following — both are robust against un-backfilled legacy data:
                  • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
                  • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
                    
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
                    
presence.
                  A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
                  
but the call-site fix above is sufficient and avoids touching user data on read paths.
                  Bug 2 — unrelated wiki pages get reformatted
                  Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
                  39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
                  Example (from a concept page unrelated to ollama):
                  - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
                  Root cause
                  cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
                  openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
                  
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
                  
get swept up too.
                  Impact
                  • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
                  • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
                  • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
                    
refactoring.
                  Suggested fix (preferred)
                  Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
                  {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
                  
without sweeping the rest of the KB.
                  Alternatives
                  • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
                  • Make the global pass opt-in via a flag (e.g. --lint), default off.
                  Metadata
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                  Assignees
                  No one assigned
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, 'i');
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function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
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lastUrl = location.href;
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observer.observe(document.body, { childList: true, subtree: true });
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}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
                      Skip to content
                      openkb remove leaves orphan hash and reformats unrelated wiki #58
                      Closed
                      #62
                      Closed
                      openkb remove leaves orphan hash and reformats unrelated wiki#58
                      #62
                      Description
                      @wooogy-dev
                      wooogy-dev
                      opened on May 18, 2026
                      A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
                      
they share a single repro, but they have different root causes and need separate fixes.
                      Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
                      Repro
                      1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
                        
wikilinks.
                      2. openkb remove <that-doc> (e.g. openkb remove ollama).
                      3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
                      Bug 1 — hash entry is not removed for docs ingested before PR #51
                      cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
                      
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
                      Root cause
                      Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
                      
into the registry. However, entries that already existed in hashes.json before that commit were not
                      
backfilled                       — they still carry only {name, type}.
                      HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
                      False. The method silently returns False; nothing in the call chain checks the return value.
                      Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
                      
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
                      
is invisible at the surface.
                      Suggested fix
                      Either of the following — both are robust against un-backfilled legacy data:
                      • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
                      • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
                        
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
                        
presence.
                      A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
                      
but the call-site fix above is sufficient and avoids touching user data on read paths.
                      Bug 2 — unrelated wiki pages get reformatted
                      Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
                      39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
                      Example (from a concept page unrelated to ollama):
                      - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
                      Root cause
                      cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
                      openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
                      
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
                      
get swept up too.
                      Impact
                      • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
                      • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
                      • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
                        
refactoring.
                      Suggested fix (preferred)
                      Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
                      {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
                      
without sweeping the rest of the KB.
                      Alternatives
                      • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
                      • Make the global pass opt-in via a flag (e.g. --lint), default off.
                      Metadata
                      Metadata
                      Assignees
                      No one assigned
                        Labels
                        No labels
                        No labels
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                        No type
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                        No projects
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                          No milestone
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                          None yet
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                          No branches or pull requests
                          Issue actions
                          
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
                          Skip to content
                          openkb remove leaves orphan hash and reformats unrelated wiki #58
                          Closed
                          #62
                          Closed
                          openkb remove leaves orphan hash and reformats unrelated wiki#58
                          #62
                          Description
                          @wooogy-dev
                          wooogy-dev
                          opened on May 18, 2026
                          A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
                          
they share a single repro, but they have different root causes and need separate fixes.
                          Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
                          Repro
                          1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
                            
wikilinks.
                          2. openkb remove <that-doc> (e.g. openkb remove ollama).
                          3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
                          Bug 1 — hash entry is not removed for docs ingested before PR #51
                          cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
                          
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
                          Root cause
                          Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
                          
into the registry. However, entries that already existed in hashes.json before that commit were not
                          
backfilled                           — they still carry only {name, type}.
                          HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
                          False. The method silently returns False; nothing in the call chain checks the return value.
                          Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
                          
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
                          
is invisible at the surface.
                          Suggested fix
                          Either of the following — both are robust against un-backfilled legacy data:
                          • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
                          • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
                            
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
                            
presence.
                          A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
                          
but the call-site fix above is sufficient and avoids touching user data on read paths.
                          Bug 2 — unrelated wiki pages get reformatted
                          Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
                          39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
                          Example (from a concept page unrelated to ollama):
                          - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
                          Root cause
                          cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
                          openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
                          
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
                          
get swept up too.
                          Impact
                          • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
                          • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
                          • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
                            
refactoring.
                          Suggested fix (preferred)
                          Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
                          {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
                          
without sweeping the rest of the KB.
                          Alternatives
                          • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
                          • Make the global pass opt-in via a flag (e.g. --lint), default off.
                          Metadata
                          Metadata
                          Assignees
                          No one assigned
                            Labels
                            No labels
                            No labels
                            Type
                            No type
                            Projects
                            No projects
                              Milestone
                              No milestone
                              Relationships
                              None yet
                              Development
                              No branches or pull requests
                              Issue actions
                              
, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
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/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
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filter: invert(1) hue-rotate(180deg) !important;
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[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
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.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
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filter: none !important;
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filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
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openkb remove leaves orphan hash and reformats unrelated wiki · Issue #58 · VectifyAI/OpenKB · GitHub
                              Skip to content
                              openkb remove leaves orphan hash and reformats unrelated wiki #58
                              Closed
                              #62
                              Closed
                              openkb remove leaves orphan hash and reformats unrelated wiki#58
                              #62
                              Description
                              @wooogy-dev
                              wooogy-dev
                              opened on May 18, 2026
                              A single openkb remove <doc> run surfaces two independent bugs at once. Reporting them together because
                              
they share a single repro, but they have different root causes and need separate fixes.
                              Follow-up to #41 — both are regressions in the implementation shipped by PR #51.
                              Repro
                              1. KB containing at least one document ingested before PR feat(cli): add openkb remove to safely delete a document (closes #41) #51 (hashes.json entry has only {name, type}, no doc_name key) and a handful of LLM-generated concept pages with pre-existing dangling
                                
wikilinks.
                              2. openkb remove <that-doc> (e.g. openkb remove ollama).
                              3. Observed: removal "succeeds" but git status / hashes.json show the symptoms below.
                              Bug 1 — hash entry is not removed for docs ingested before PR #51
                              cat .openkb/hashes.json still contains the removed doc's entry after openkb remove reports success.
                              
Re-running openkb add <same-file> is then incorrectly treated as a duplicate via the SHA dedup.
                              Root cause
                              Commit c504e26 (within this same PR) fixed add_single_file so newly-ingested docs persist doc_name
                              
into the registry. However, entries that already existed in hashes.json before that commit were not
                              
backfilled                               — they still carry only {name, type}.
                              HashRegistry.remove_by_doc_name (openkb/state.py:44-51) matches with meta.get("doc_name") == doc_name. For un-backfilled legacy entries the comparison evaluates to None == "<slug>" → always
                              False. The method silently returns False; nothing in the call chain checks the return value.
                              Meanwhile cli.py:670 (doc_name = meta.get("doc_name") or Path(name).stem) does fall back to the
                              
filename stem to drive every other step, so summary/source/concept/index removal succeeds and the failure
                              
is invisible at the surface.
                              Suggested fix
                              Either of the following — both are robust against un-backfilled legacy data:
                              • Add a fallback in remove_by_doc_name that also matches when Path(meta["name"]).stem == doc_name, OR
                              • Introduce remove_by_hash(file_hash) and call it from cli.py:842 since the CLI already has the
                                
matched hash in hand. Preferred — eliminates the slug round-trip and works regardless of doc_name
                                
presence.
                              A one-shot migration that backfills doc_name on the next openkb invocation would also clean this up,
                              
but the call-site fix above is sufficient and avoids touching user data on read paths.
                              Bug 2 — unrelated wiki pages get reformatted
                              Removing a single doc produces a sprawling diff. In my repro, removing one ollama.md produced a
                              39-file / 1254-line diff; 27 of those were concept pages that didn't list ollama as a source.
                              Example (from a concept page unrelated to ollama):
                              - **Knowledge access**: agents need curated context such as [[LLM Wiki]] + **Knowledge access**: agents need curated context such as LLM Wiki 
                              Root cause
                              cli.py:815 calls fix_broken_links(wiki_dir) over the entire wiki on every remove.
                              openkb/lint.py:fix_broken_links strips every dangling wikilink in the KB, not only the ones created by
                              
this removal. Pre-existing ghost links (LLM-generated, hand-edited, links to not-yet-added concepts, etc.)
                              
get swept up too.
                              Impact
                              • Removal commits are unreadable — actual deletion effects are buried under unrelated reformat noise.
                              • Users lose [[wikilinks]] they may want to keep (e.g. links to a concept they plan to add later).
                              • Violates least-surprise: the command name says "remove one doc," but the diff shows wiki-wide
                                
refactoring.
                              Suggested fix (preferred)
                              Limit ghost-link stripping to files actually touched by this removal: concept_result["modified"] ∪
                              {index.md}. Preserves the original PR #49 intent (clean up dangling links the removal just created)
                              
without sweeping the rest of the KB.
                              Alternatives
                              • Snapshot the global ghost set before/after the removal and strip only the newly-introduced ghosts.
                              • Make the global pass opt-in via a flag (e.g. --lint), default off.
                              Metadata
                              Metadata
                              Assignees
                              No one assigned
                                Labels
                                No labels
                                No labels
                                Type
                                No type
                                Projects
                                No projects
                                  Milestone
                                  No milestone
                                  Relationships
                                  None yet
                                  Development
                                  No branches or pull requests
                                  Issue actions