org-element-parse-buffer 4.5x slower in Doom vs emacs -q

[cashpw]

I confirm that...

• I have searched the issue tracker, documentation, FAQ, Discourse, and Google, in case this issue has already been reported/resolved.
• I have read "How to Debug Issues", and will use it to provide as much information about this issue as possible.
• The issue can be reproduced on the latest available commit of Doom.
• The issue can be reproduced on a stable release of Emacs, such as 27, 28, or 29. (Unstable versions end in .50, .60, or .9x)

Expected behavior

With emacs -q on a 15k line org-roam node (note this is an older version of the file):

#+begin_src emacs-lisp
(defmacro measure-time (&rest body)
  "Measure the time it takes to evaluate BODY.

Reference:https://stackoverflow.com/q/23622296"
  `(let ((start-time (current-time)))
     ,@body
     (message "%.06f"
              (float-time (time-since start-time)))))

(measure-time
 (org-element-parse-buffer))
#+end_src

#+RESULTS:
: 0.4...

Current behavior

With Doom Emacs configured with example templates on a 15k line org-roam node (note this is an older version of the file):

#+begin_src emacs-lisp
(defmacro measure-time (&rest body)
  "Measure the time it takes to evaluate BODY.

Reference:https://stackoverflow.com/q/23622296"
  `(let ((start-time (current-time)))
     ,@body
     (message "%.06f"
              (float-time (time-since start-time)))))

(measure-time
 (org-element-parse-buffer))
#+end_src

#+RESULTS:
: 1.830191

Steps to reproduce

Run babel blocks above.

System Information

https://pastebin.com/Q0tU1vqA

[cashpw]

Memory profile in doomemacs

                                                                264,658,893  99% - command-execute
                                                                264,658,893  99%  - funcall-interactively
                                                                264,658,893  99%   - +org/dwim-at-point
                                                                264,658,893  99%    - if
                                                                264,658,893  99%     - let*
                                                                264,658,893  99%      - cond
                                                                264,658,893  99%       - let
                                                                264,658,893  99%        - org-babel-execute-src-block
                                                                264,658,893  99%         - org-babel-execute:emacs-lisp
                                                                264,658,893  99%          - progn
                                                                264,658,893  99%           - let
                                                                263,818,534  99%            - setq
                                                                263,818,534  99%             - measure-time
                                                                263,818,534  99%              - let
                                                                263,817,737  99%               - org-element-parse-buffer
                                                                263,817,737  99%                - save-excursion
                                                                263,817,737  99%                 - let
                                                                263,807,449  99%                  - org-element--parse-elements
                                                                263,807,449  99%                   - save-excursion
                                                                263,807,449  99%                    - let
                                                                263,807,449  99%                     - while
                                                                263,807,449  99%                      - if
                                                                263,807,449  99%                       - let*
                                                                263,807,449  99%                        - cond
                                                                263,807,449  99%                         - org-element--parse-elements
                                                                263,807,449  99%                          - save-excursion
                                                                263,807,449  99%                           - let
                                                                263,708,617  99%                            - while
                                                                263,708,617  99%                             - if
                                                                263,529,097  99%                              - let*
                                                                211,672,526  79%                               - org-element-copy
                                                                130,067,904  49%                                - if
                                                                130,067,904  49%                                 - progn
                                                                129,835,584  49%                                  - let
                                                                129,582,144  48%                                   - cond
                                                                129,582,144  48%                                    - let
                                                                129,335,040  48%                                     - let
                                                                124,238,784  46%                                      - org-element-map
                                                                109,725,328  41%                                       - let*
                                                                108,404,272  40%                                        - let
                                                                105,553,072  39%                                         - setq
                                                                105,430,576  39%                                          - function
                                                                 99,054,624  37%                                           - cconv-make-interpreted-closure
                                                                 54,627,936  20%                                            - macroexpand-all
                                                                 54,391,392  20%                                             - macroexp--expand-all
                                                                 53,785,248  20%                                              - macroexp--all-forms
                                                                 53,551,872  20%                                               - macroexp--expand-all
                                                                 52,675,392  19%                                                - macroexp--all-forms
                                                                 52,445,184  19%                                                 - macroexp--expand-all
                                                                 51,732,384  19%                                                  - macroexp--all-clauses
                                                                 51,266,688  19%                                                   - macroexp--all-forms
                                                                 48,566,496  18%                                                    - macroexp--expand-all
                                                                 40,916,832  15%                                                     - macroexp--all-forms
                                                                 37,053,984  13%                                                      - macroexp--expand-all
                                                                 36,316,896  13%                                                       - macroexp--all-forms
                                                                 33,200,640  12%                                                        - macroexp--expand-all
                                                                 29,719,008  11%                                                         - macroexp--all-forms
                                                                 27,277,536  10%                                                          - macroexp--expand-all
                                                                 26,558,400  10%                                                           - macroexp--all-forms
                                                                 25,095,840   9%                                                            - macroexp--expand-all
                                                                 24,849,792   9%                                                             - macroexp--all-forms
                                                                 24,849,792   9%                                                              - macroexp--expand-all
                                                                 24,849,792   9%                                                               - macroexp--all-forms
                                                                 24,849,792   9%                                                                - macroexp--expand-all
                                                                 24,849,792   9%                                                                 - macroexp--all-clauses
                                                                 24,366,144   9%                                                                  - macroexp--all-forms
                                                                 22,406,208   8%                                                                   - macroexp--expand-all
                                                                 21,533,952   8%                                                                    - macroexp--all-forms
                                                                 17,426,112   6%                                                                     - macroexp--expand-all
                                                                 16,094,496   6%                                                                      - macroexp--all-forms
                                                                 14,421,792   5%                                                                       - macroexp--expand-all
                                                                 14,071,200   5%                                                                        - macroexp--all-forms
                                                                 13,103,904   4%                                                                         - macroexp--expand-all
                                                                  9,460,704   3%                                                                          - macroexp--all-forms
                                                                  8,231,520   3%                                                                           - macroexp--expand-all
                                                                  5,819,616   2%                                                                            - macroexp--all-forms
                                                                  4,134,240   1%                                                                             - macroexp--expand-all
                                                                  2,054,976   0%                                                                              - macroexp--all-forms
                                                                  1,077,120   0%                                                                               - macroexp--expand-all
                                                                    496,320   0%                                                                                  macroexp--all-forms
                                                                    493,152   0%                                                                              - macroexp--expand-all
                                                                    493,152   0%                                                                                 macroexp--all-forms
                                                                    491,040   0%                                                                              - macroexp--all-clauses
                                                                    491,040   0%                                                                                 macroexp--all-forms
                                                                    954,624   0%                                                                            - macroexp--all-clauses
                                                                    954,624   0%                                                                             - macroexp--all-forms
                                                                    483,648   0%                                                                              - macroexp--expand-all
                                                                    483,648   0%                                                                                 macroexp--all-forms
                                                                  3,155,328   1%                                                                          - macroexp--all-clauses
                                                                  3,155,328   1%                                                                           - macroexp--all-forms
                                                                  1,691,712   0%                                                                            - macroexp--expand-all
                                                                    960,960   0%                                                                               macroexp--all-forms
                                                                    485,760   0%                                                                             - macroexp--expand-all
                                                                    485,760   0%                                                                                macroexp--all-forms
                                                                    472,032   0%                                                                      - macroexp--all-clauses
                                                                    472,032   0%                                                                       - macroexp--all-forms
                                                                    238,656   0%                                                                        - macroexp--expand-all
                                                                    238,656   0%                                                                           macroexp--all-forms
                                                                    246,048   0%                                                             - macroexp--expand-all
                                                                    246,048   0%                                                                macroexp--all-forms
                                                                  2,408,736   0%                                                         - macroexp--all-clauses
                                                                  2,178,528   0%                                                          - macroexp--all-forms
                                                                  1,213,344   0%                                                           - macroexp--expand-all
                                                                    979,968   0%                                                            - macroexp--all-forms
                                                                    481,536   0%                                                             - macroexp--expand-all
                                                                    481,536   0%                                                                macroexp--all-forms
                                                                  6,550,368   2%                                                     - macroexp--all-clauses
                                                                  6,550,368   2%                                                      - macroexp--all-forms
                                                                  5,116,320   1%                                                       - macroexp--expand-all
                                                                  5,116,320   1%                                                        - macroexp--all-forms
                                                                  2,910,336   1%                                                         - macroexp--expand-all
                                                                  2,910,336   1%                                                          - macroexp--all-forms
                                                                    742,368   0%                                                           - macroexp--expand-all
                                                                    742,368   0%                                                              macroexp--all-forms
                                                                    500,544   0%                                                - macroexp--all-clauses
                                                                    500,544   0%                                                 - macroexp--all-forms
                                                                    251,328   0%                                                  - macroexp--expand-all
                                                                    251,328   0%                                                     macroexp--all-forms
                                                                 40,604,256  15%                                            - cconv-fv
                                                                 32,592,384  12%                                             - cconv-analyze-form
                                                                 29,569,056  11%                                              - cconv--analyze-function
                                                                 21,465,312   8%                                               - cconv-analyze-form
                                                                 21,213,984   8%                                                - cconv-analyze-form
                                                                 19,736,640   7%                                                 - cconv-analyze-form
                                                                 17,111,424   6%                                                  - cconv-analyze-form
                                                                 14,054,304   5%                                                   - cconv-analyze-form
                                                                 11,373,120   4%                                                    - cconv-analyze-form
                                                                  9,171,360   3%                                                     - cconv-analyze-form
                                                                  7,477,536   2%                                                      - cconv-analyze-form
                                                                  6,270,528   2%                                                       - cconv-analyze-form
                                                                  4,575,648   1%                                                        - cconv-analyze-form
                                                                  2,880,768   1%                                                         - cconv-analyze-form
                                                                  2,056,032   0%                                                          - cconv-analyze-form
                                                                  1,335,840   0%                                                           - cconv-analyze-form
                                                                    850,080   0%                                                            - cconv-analyze-form
                                                                    373,824   0%                                                               cconv-analyze-form
...

CPU profile in doomemacs

                                                                       1738  99% - ...
                                                                       1625  92%  - #<lambda 0x137082d47a64517e>
                                                                       1625  92%   - let
                                                                       1625  92%    - cond
                                                                       1625  92%     - mapc
                                                                       1621  92%      - #<lambda 0x137082d47a64517e>
                                                                       1621  92%       - let
                                                                       1617  92%        - org-element-parse-buffer
                                                                       1617  92%         - save-excursion
                                                                       1617  92%          - let
                                                                       1612  92%           - org-element--parse-elements
                                                                       1612  92%            - save-excursion
                                                                       1612  92%             - let
                                                                       1612  92%              - while
                                                                       1612  92%               - if
                                                                       1612  92%                - let*
                                                                       1612  92%                 - cond
                                                                       1612  92%                  - org-element--parse-elements
                                                                       1612  92%                   - save-excursion
                                                                       1612  92%                    - let
                                                                       1612  92%                     - while
                                                                       1612  92%                      - if
                                                                       1612  92%                       - let*
                                                                       1596  91%                        - cond
                                                                       1596  91%                         - org-element--parse-elements
                                                                       1588  90%                          - save-excursion
                                                                       1580  90%                           - let
                                                                       1576  90%                            - while
                                                                       1576  90%                             - if
                                                                       1576  90%                              - let*
                                                                       1556  88%                               - org-element-copy
                                                                        864  49%                                - if
                                                                        864  49%                                 - progn
                                                                        860  49%                                  - let
                                                                        852  48%                                   - cond
                                                                        848  48%                                    - let
                                                                        848  48%                                     - let
                                                                        832  47%                                      - org-element-map
                                                                        660  37%                                       - let*
                                                                        644  36%                                        - let
                                                                        616  35%                                         - setq
                                                                        612  34%                                          - function
                                                                        572  32%                                           - cconv-make-interpreted-closure
                                                                        416  23%                                            - macroexpand-all
                                                                        416  23%                                             - macroexp--expand-all
                                                                        412  23%                                              - macroexp--all-forms
                                                                        412  23%                                               - macroexp--expand-all
                                                                        412  23%                                                - macroexp--all-forms
                                                                        412  23%                                                 - macroexp--expand-all
                                                                        408  23%                                                  - macroexp--all-clauses
                                                                        404  23%                                                   - macroexp--all-forms
                                                                        396  22%                                                    - macroexp--expand-all
                                                                        328  18%                                                     - macroexp--all-forms
                                                                        308  17%                                                      - macroexp--expand-all
                                                                        268  15%                                                       - macroexp--all-forms
                                                                        268  15%                                                        - macroexp--expand-all
                                                                        196  11%                                                         - macroexp--all-forms
                                                                        188  10%                                                          - macroexp--expand-all
                                                                        136   7%                                                           - macroexp--all-forms
                                                                        136   7%                                                            - macroexp--expand-all
                                                                        116   6%                                                             - macroexp--all-forms
                                                                        116   6%                                                              - macroexp--expand-all
                                                                        104   5%                                                               - macroexp--all-forms
                                                                        100   5%                                                                - macroexp--expand-all
                                                                         88   5%                                                                 - macroexp--all-clauses
                                                                         88   5%                                                                  - macroexp--all-forms
                                                                         84   4%                                                                   - macroexp--expand-all
                                                                         56   3%                                                                    - macroexp--all-forms
                                                                         52   2%                                                                     - macroexp--expand-all
                                                                         24   1%                                                                      - macroexp--all-forms
                                                                         16   0%                                                                       - macroexp--expand-all
                                                                          4   0%                                                                          macroexp-macroexpand
                                                                          4   0%                                                                          macroexp--all-forms
                                                                          8   0%                                                                      - macroexp--all-clauses
                                                                          8   0%                                                                       - macroexp--all-forms
                                                                          8   0%                                                                        - macroexp--expand-all
                                                                          4   0%                                                                           macroexp--all-forms
                                                                          4   0%                                                                      macroexp--expand-all
                                                                          4   0%                                                               - macroexp--all-clauses
                                                                          4   0%                                                                  macroexp--all-forms
                                                                          4   0%                                                               macroexp--expand-all
                                                                          4   0%                                                               macroexp--all-clauses
                                                                          4   0%                                                               macroexp-macroexpand
                                                                         36   2%                                                           - macroexp--all-clauses
                                                                         32   1%                                                            - macroexp--all-forms
                                                                         28   1%                                                             - macroexp--expand-all
                                                                          4   0%                                                                macroexp-macroexpand
                                                                          4   0%                                                              - macroexp--expand-all
                                                                          4   0%                                                                 macroexp--all-forms
                                                                          4   0%                                                                macroexp--all-forms
                                                                         24   1%                                                         - macroexp--all-clauses
                                                                         24   1%                                                          - macroexp--all-forms
                                                                         16   0%                                                           - macroexp--expand-all
                                                                          4   0%                                                              macroexp--all-forms
                                                                          4   0%                                                           macroexp-macroexpand
                                                                          4   0%                                                         macroexp-macroexpand
                                                                         44   2%                                                     - macroexp--all-clauses
                                                                         44   2%                                                      - macroexp--all-forms
                                                                         40   2%                                                       - macroexp--expand-all
                                                                         40   2%                                                        - macroexp--all-forms

...

[cashpw]

Memory profile in `emacs -q`

    135,193,280 100% - command-execute
    135,193,280 100%  - funcall-interactively
    135,193,280 100%   - org-ctrl-c-ctrl-c
    135,193,280 100%    - org-babel-execute-src-block
    135,193,280 100%     - org-babel-execute:emacs-lisp
    135,193,280 100%      - progn
    135,193,280 100%       - let
    131,508,297  97%        - setq
    131,508,297  97%         - measure-time
    131,508,297  97%          - let
    131,508,196  97%           - org-element-parse-buffer
    131,495,340  97%            - org-element--parse-elements
    131,369,556  97%             - org-element--parse-elements
     92,512,213  68%              - org-element--current-element
     88,279,246  65%               - org-element-headline-parser
     41,379,638  30%                - org-element--parse-objects
     38,172,702  28%                 - org-element--object-lex
     35,443,872  26%                  - org-element-link-parser
      6,655,448   4%                   - org-link-unescape
        386,704   0%                      replace-regexp-in-string
        556,120   0%                     org-link-expand-abbrev
        432,864   0%                     replace-regexp-in-string
          3,262   0%                  + org-element-italic-parser
          3,104   0%                    org-element-citation-parser
      1,674,704   1%                 + org-element--parse-objects
      2,950,288   2%                + rx-to-string
      1,573,832   1%                  org-element--get-node-properties
      1,380,416   1%                  replace-regexp-in-string
        133,056   0%               + org-get-limited-outline-regexp
         12,568   0%               + org-element-src-block-parser
          7,200   0%                 org-element--collect-affiliated-keywords
          5,124   0%                 org-element-paragraph-parser
          4,096   0%                 org-element-section-parser
          3,072   0%                 org-element-keyword-parser
          2,469   0%                 org-element-table-parser
          1,024   0%                 org-element-property-drawer-parser
          1,024   0%                 org-element-fixed-width-parser
     33,014,415  24%              + org-element--parse-elements
      4,989,200   3%              + org-element-copy
         66,528   0%                apply
          5,416   0%              + org-element--parse-objects
         66,648   0%             + org-element--current-element
          1,056   0%               org-element-copy
         12,856   0%            + org-element-org-data-parser
             16   0%           + message
      3,684,352   2%          profiler-report
            631   0%          profiler-start
              0   0%   ...

CPU profile in `emacs -q`

         436  96% - command-execute
         436  96%  - funcall-interactively
         436  96%   - org-ctrl-c-ctrl-c
         436  96%    - org-babel-execute-src-block
         436  96%     - org-babel-execute:emacs-lisp
         436  96%      - progn
         436  96%       - let
         428  94%        - setq
         428  94%         - measure-time
         428  94%          - let
         428  94%           - org-element-parse-buffer
         428  94%            - org-element--parse-elements
         416  91%             - org-element--parse-elements
         236  51%              - org-element--current-element
         216  47%               - org-element-headline-parser
         112  24%                - org-element--parse-objects
          80  17%                 - org-element--object-lex
          60  13%                  - org-element-link-parser
          16   3%                     org-link-unescape
           4   0%                     org-link-expand-abbrev
          28   6%                 - org-element--parse-objects
          20   4%                    org-element--object-lex
          12   2%                  org-element--get-node-properties
           4   0%                  org-element--get-time-properties
         156  34%              - org-element--parse-elements
          80  17%               - org-element--parse-elements
          32   7%                - org-element--parse-elements
          16   3%                 - org-element--current-element
           4   0%                    org-element-node-property-parser
          12   2%                   org-element-copy
           4   0%                 - org-element--parse-elements
           4   0%                    org-element--current-element
          24   5%                - org-element--current-element
           4   0%                   org-element--cache-find
          12   2%                  org-element-copy
          56  12%               - org-element--current-element
          28   6%                  org-element-section-parser
           4   0%                  org-element--cache-find
          12   2%               - org-element-copy
           4   0%                  org-element-map
          12   2%                org-element-copy
           4   0%             - org-element--current-element
           4   0%                org-element-headline-parser
           4   0%          profiler-start
           4   0%          profiler-report
          18   3% - ...
          18   3%    Automatic GC

[cashpw]

• I'm not sure why the profiler is more detailed (i.e. mentions the let* and while, etc)
• The big difference, as far as I can see, is org-element-copy being 79% in doomemacs versus 3% in emacs -q

[hlissner]

I haven't had time to properly bisect org, but it seems that these performance issues were introduced during recent bumps. A brief history:

• emacs-straight/org-mode@7a6bb09 was the last known "fast" commit (what the org module was pinned to until March 29th).
• In 5f5a163, I bumped it to emacs-straight/org-mode@e9c288d, which introduced a lot of performance problems in Org buffers.
• I reverted org to emacs-straight/org-mode@5bdfc02c6fa1 in 5b7d676 to mitigate this.

That's markedly improved the worst cases, but if this issue is any indications, I'm guessing we're not totally out of the woods.

There is a lot of work between emacs-straight/org-mode@7a6bb09 and their HEAD (emacs-straight/org-mode@1ae978f) so it's difficult to pin-point the cause, but here are some things for you to try:

• Unpin org. Maybe this has been addressed upstream recently.
• Try one of these commits that predate our current pin (emacs-straight/org-mode@e9c288d). It'd help me zero in on where the problem began, and may perhaps inform a bug report upstream:
  • emacs-straight/org-mode@bc0e14a (Feb 11)
  • emacs-straight/org-mode@fe9bc9e (Feb 28)
  • emacs-straight/org-mode@28dc5dd (Mar 8)
  • emacs-straight/org-mode@50c51b9 (Mar 22)
  • emacs-straight/org-mode@5ff4d54 (Mar 24)
  • emacs-straight/org-mode@5bdfc02 (Mar 26) (Where the org module is pinned now)

[cashpw]

Unpin org. Maybe this has been addressed upstream recently.

#7835 (comment)

I added the following to packages.el

(unpin! org org-contrib)

and re-ran the benchmark:

#+begin_src emacs-lisp
(benchmark 1 '(org-element-parse-buffer))
#+end_src

#+RESULTS:
: Elapsed time: 1.010177s (0.205194s in 1 GCs)

Improved, but still ~2.25x. I'll dig in later tonight.

[hlissner]

I mean some slow down is unavoidable. Vanilla Doom enables a few expensive features that are disabled in vanilla Org/Emacs, like org-startup-indented (i.e. org-indent-mode), org-fontify-quote-and-verse-blocks, org-startup-folded != showeverything, etc, so without establishing some parity between the two test cases, it's hard to tell where the "too slow" cut-off point is.

[cashpw]

That's a good point, and maybe I'm going about this the wrong way. This issue is an XY problem. The original problem is that this file takes a long time to save. I had identified org-element-parse-buffer as a primary contributor.

#+begin_src emacs-lisp
(defmacro measure-time (&rest body)
  "Measure the time it takes to evaluate BODY.

Reference:https://stackoverflow.com/q/23622296"
  `(let ((start-time (current-time)))
     ,@body
     (message "%.06f"
              (float-time (time-since start-time)))))
(measure-time
 (save-buffer))
#+end_src

#+RESULTS:
: 13.644738

This is my largest file by far, so it's an outlier. Maybe a better course would be to disable expensive functionality in this buffer in particular.

#+begin_src emacs-lisp
`(,(length (org-map-entries t "LEVEL=1"))
,(length (org-map-entries t "LEVEL=2"))
,(length (org-map-entries t "LEVEL=3"))
,(length (org-map-entries t "LEVEL=4"))
)
#+end_src

#+RESULTS:
| 9 | 3910 | 29 | 0 |

#+begin_src emacs-lisp :tangle config-personal.el :results none
(set-eglot-client!
 'org-mode
 '("vale-ls"))

(add-hook! 'org-mode-hook
           #'eglot-ensure)
#+end_src

Looks like org-roam is the primary contributor. I copied the file into a non-org-roam directory, /tmp, and (save-buffer) runs in ~1 second.

[cashpw]

I’ve improved performance dramatically (down to <1s from ~14s) by:

1. Disabling org-encrypt-entries, which called out to org-element-cache-map which accounted for ~94% of the memory (per the profiler):

   (after! org-crypt
     (advice-add
      'org-encrypt-entries
      :override #'ignore))

2. Limit org-roam-link-replace-at-point (through org-roam-link-replace-all) to roam: links:

   (after! org-roam
     ;; Override to only replace if it's a roam link.
     (defun org-roam-link-replace-all ()
       "Replace all \"roam:\" links in buffer with \"id:\" links."
       (interactive)
       (org-with-point-at 1
         (while (re-search-forward org-link-bracket-re nil t)
           (when (s-starts-with-p
                  "roam:"
                  (match-string 1))
             (org-roam-link-replace-at-point))))))

3. Disable org-roam auto-sync and instead sync when afk:

   (after! org-roam
     ;; Don't auto-sync
     (org-roam-db-autosync-disable)
     ;; Sync when I'm away from keyoard.
     (setq
      cashpw/org-roam-sync-timer (run-with-idle-timer
                                  60
                                  t
                                  (lambda ()
                                    (let* ((org-roam-directory
                                            cashpw/path--notes-dir)
                                           (org-roam-db-location
                                            (expand-file-name
                                             "org-roam.db"
                                             org-roam-directory)))
                                      (message "Syncing roam database ")
                                      (org-roam-db-sync))))))

[hlissner]

Good finds. I'll look into adapting them to the Org module. I'll keep this open until I do.

[yantar92]

FYI, the CPU profile indicates that Org mode is not even byte-compiled.

[meedstrom]

And FYI, org-roam-db-autosync-mode is inexactly named; it does more than just resync the file on save. So you might want to think about that.

Here's what it does when enabled -- all pretty straightforward except the find-file hook:

      (add-hook 'find-file-hook  #'org-roam-db-autosync--setup-file-h)
      (add-hook 'kill-emacs-hook #'org-roam-db--close-all)
      (advice-add #'rename-file :after  #'org-roam-db-autosync--rename-file-a)
      (advice-add #'delete-file :before #'org-roam-db-autosync--delete-file-a)

The find-file-hook, in turn, runs org-roam-find-file-hook if it's an org-roam file, and that hook contains these functions:

(org-roam-buffer--setup-redisplay-h 
 org-roam--register-completion-functions-h
 org-roam--replace-roam-links-on-save-h
 org-roam-db-autosync--setup-update-on-save-h)

So among other things, you are entirely disabling the replace-roam-links functionality, so the limitation you did above is moot ;-)

I have some experience fiddling with this thing, so what I would actually suggest is to keep autosync-mode on, don't reinvent the wheel, and then just set the option org-roam-db-update-on-save to nil.